diff --git a/SKILL.md b/SKILL.md
index 7e2acdabf..8c1ff4dfb 100644
--- a/SKILL.md
+++ b/SKILL.md
@@ -377,10 +377,13 @@ _BRAIN_SYNC_MODE=$("$_BRAIN_CONFIG_BIN" get artifacts_sync_mode 2>/dev/null || e
 # Detect remote-MCP mode (Path 4 of /setup-gbrain). Local artifacts sync is
 # a no-op in remote mode; the brain server pulls from GitHub/GitLab on its
 # own cadence. Read claude.json directly to keep this preamble fast (no
-# subprocess to claude CLI on every skill start).
+# subprocess to claude CLI on every skill start). Both registration scopes
+# are read (#2499): user scope, then the nearest-ancestor project scope.
 _GBRAIN_MCP_MODE="none"
+_GBRAIN_MCP_ENTRY=""
 if command -v jq >/dev/null 2>&1 && [ -f "$HOME/.claude.json" ]; then
-  _GBRAIN_MCP_TYPE=$(jq -r '.mcpServers.gbrain.type // .mcpServers.gbrain.transport // empty' "$HOME/.claude.json" 2>/dev/null)
+  _GBRAIN_MCP_ENTRY=$(jq -c --arg cwd "$PWD" '.mcpServers.gbrain // ((.projects // {}) | to_entries | map(select((.key as $k | $cwd == $k or ($cwd | startswith($k + "/"))) and ((try .value.mcpServers.gbrain catch null) != null))) | sort_by(.key | length) | last | .value.mcpServers.gbrain) // empty' "$HOME/.claude.json" 2>/dev/null)
+  _GBRAIN_MCP_TYPE=$(printf '%s' "$_GBRAIN_MCP_ENTRY" | jq -r '.type // .transport // empty' 2>/dev/null)
   case "$_GBRAIN_MCP_TYPE" in
     url|http|sse) _GBRAIN_MCP_MODE="remote-http" ;;
     stdio) _GBRAIN_MCP_MODE="local-stdio" ;;
@@ -415,7 +418,7 @@ fi
 if [ "$_GBRAIN_MCP_MODE" = "remote-http" ]; then
   # Remote-MCP mode: local artifacts sync is a no-op (brain admin's server
   # pulls from GitHub/GitLab). Show the user this is by design, not broken.
-  _GBRAIN_HOST=$(jq -r '.mcpServers.gbrain.url // empty' "$HOME/.claude.json" 2>/dev/null | sed -E 's|^https?://([^/:]+).*|\1|' | head -1 | tr -cd 'A-Za-z0-9._-')
+  _GBRAIN_HOST=$(printf '%s' "${_GBRAIN_MCP_ENTRY:-}" | jq -r '.url // empty' 2>/dev/null | sed -E 's|^https?://([^/:]+).*|\1|' | head -1 | tr -cd 'A-Za-z0-9._-')
   echo "ARTIFACTS_SYNC: remote-mode (managed by brain server ${_GBRAIN_HOST:-remote})"
 elif [ -d "$_GSTACK_HOME/.git" ] && [ "$_BRAIN_SYNC_MODE" != "off" ]; then
   _BRAIN_QUEUE_DEPTH=0
diff --git a/autoplan/SKILL.md b/autoplan/SKILL.md
index 66c013051..f81dc72a5 100644
--- a/autoplan/SKILL.md
+++ b/autoplan/SKILL.md
@@ -512,10 +512,13 @@ _BRAIN_SYNC_MODE=$("$_BRAIN_CONFIG_BIN" get artifacts_sync_mode 2>/dev/null || e
 # Detect remote-MCP mode (Path 4 of /setup-gbrain). Local artifacts sync is
 # a no-op in remote mode; the brain server pulls from GitHub/GitLab on its
 # own cadence. Read claude.json directly to keep this preamble fast (no
-# subprocess to claude CLI on every skill start).
+# subprocess to claude CLI on every skill start). Both registration scopes
+# are read (#2499): user scope, then the nearest-ancestor project scope.
 _GBRAIN_MCP_MODE="none"
+_GBRAIN_MCP_ENTRY=""
 if command -v jq >/dev/null 2>&1 && [ -f "$HOME/.claude.json" ]; then
-  _GBRAIN_MCP_TYPE=$(jq -r '.mcpServers.gbrain.type // .mcpServers.gbrain.transport // empty' "$HOME/.claude.json" 2>/dev/null)
+  _GBRAIN_MCP_ENTRY=$(jq -c --arg cwd "$PWD" '.mcpServers.gbrain // ((.projects // {}) | to_entries | map(select((.key as $k | $cwd == $k or ($cwd | startswith($k + "/"))) and ((try .value.mcpServers.gbrain catch null) != null))) | sort_by(.key | length) | last | .value.mcpServers.gbrain) // empty' "$HOME/.claude.json" 2>/dev/null)
+  _GBRAIN_MCP_TYPE=$(printf '%s' "$_GBRAIN_MCP_ENTRY" | jq -r '.type // .transport // empty' 2>/dev/null)
   case "$_GBRAIN_MCP_TYPE" in
     url|http|sse) _GBRAIN_MCP_MODE="remote-http" ;;
     stdio) _GBRAIN_MCP_MODE="local-stdio" ;;
@@ -550,7 +553,7 @@ fi
 if [ "$_GBRAIN_MCP_MODE" = "remote-http" ]; then
   # Remote-MCP mode: local artifacts sync is a no-op (brain admin's server
   # pulls from GitHub/GitLab). Show the user this is by design, not broken.
-  _GBRAIN_HOST=$(jq -r '.mcpServers.gbrain.url // empty' "$HOME/.claude.json" 2>/dev/null | sed -E 's|^https?://([^/:]+).*|\1|' | head -1 | tr -cd 'A-Za-z0-9._-')
+  _GBRAIN_HOST=$(printf '%s' "${_GBRAIN_MCP_ENTRY:-}" | jq -r '.url // empty' 2>/dev/null | sed -E 's|^https?://([^/:]+).*|\1|' | head -1 | tr -cd 'A-Za-z0-9._-')
   echo "ARTIFACTS_SYNC: remote-mode (managed by brain server ${_GBRAIN_HOST:-remote})"
 elif [ -d "$_GSTACK_HOME/.git" ] && [ "$_BRAIN_SYNC_MODE" != "off" ]; then
   _BRAIN_QUEUE_DEPTH=0
diff --git a/benchmark-models/SKILL.md b/benchmark-models/SKILL.md
index 71608c5a0..75e7e5128 100644
--- a/benchmark-models/SKILL.md
+++ b/benchmark-models/SKILL.md
@@ -381,10 +381,13 @@ _BRAIN_SYNC_MODE=$("$_BRAIN_CONFIG_BIN" get artifacts_sync_mode 2>/dev/null || e
 # Detect remote-MCP mode (Path 4 of /setup-gbrain). Local artifacts sync is
 # a no-op in remote mode; the brain server pulls from GitHub/GitLab on its
 # own cadence. Read claude.json directly to keep this preamble fast (no
-# subprocess to claude CLI on every skill start).
+# subprocess to claude CLI on every skill start). Both registration scopes
+# are read (#2499): user scope, then the nearest-ancestor project scope.
 _GBRAIN_MCP_MODE="none"
+_GBRAIN_MCP_ENTRY=""
 if command -v jq >/dev/null 2>&1 && [ -f "$HOME/.claude.json" ]; then
-  _GBRAIN_MCP_TYPE=$(jq -r '.mcpServers.gbrain.type // .mcpServers.gbrain.transport // empty' "$HOME/.claude.json" 2>/dev/null)
+  _GBRAIN_MCP_ENTRY=$(jq -c --arg cwd "$PWD" '.mcpServers.gbrain // ((.projects // {}) | to_entries | map(select((.key as $k | $cwd == $k or ($cwd | startswith($k + "/"))) and ((try .value.mcpServers.gbrain catch null) != null))) | sort_by(.key | length) | last | .value.mcpServers.gbrain) // empty' "$HOME/.claude.json" 2>/dev/null)
+  _GBRAIN_MCP_TYPE=$(printf '%s' "$_GBRAIN_MCP_ENTRY" | jq -r '.type // .transport // empty' 2>/dev/null)
   case "$_GBRAIN_MCP_TYPE" in
     url|http|sse) _GBRAIN_MCP_MODE="remote-http" ;;
     stdio) _GBRAIN_MCP_MODE="local-stdio" ;;
@@ -419,7 +422,7 @@ fi
 if [ "$_GBRAIN_MCP_MODE" = "remote-http" ]; then
   # Remote-MCP mode: local artifacts sync is a no-op (brain admin's server
   # pulls from GitHub/GitLab). Show the user this is by design, not broken.
-  _GBRAIN_HOST=$(jq -r '.mcpServers.gbrain.url // empty' "$HOME/.claude.json" 2>/dev/null | sed -E 's|^https?://([^/:]+).*|\1|' | head -1 | tr -cd 'A-Za-z0-9._-')
+  _GBRAIN_HOST=$(printf '%s' "${_GBRAIN_MCP_ENTRY:-}" | jq -r '.url // empty' 2>/dev/null | sed -E 's|^https?://([^/:]+).*|\1|' | head -1 | tr -cd 'A-Za-z0-9._-')
   echo "ARTIFACTS_SYNC: remote-mode (managed by brain server ${_GBRAIN_HOST:-remote})"
 elif [ -d "$_GSTACK_HOME/.git" ] && [ "$_BRAIN_SYNC_MODE" != "off" ]; then
   _BRAIN_QUEUE_DEPTH=0
diff --git a/benchmark/SKILL.md b/benchmark/SKILL.md
index 1c0e27fba..10a68e818 100644
--- a/benchmark/SKILL.md
+++ b/benchmark/SKILL.md
@@ -381,10 +381,13 @@ _BRAIN_SYNC_MODE=$("$_BRAIN_CONFIG_BIN" get artifacts_sync_mode 2>/dev/null || e
 # Detect remote-MCP mode (Path 4 of /setup-gbrain). Local artifacts sync is
 # a no-op in remote mode; the brain server pulls from GitHub/GitLab on its
 # own cadence. Read claude.json directly to keep this preamble fast (no
-# subprocess to claude CLI on every skill start).
+# subprocess to claude CLI on every skill start). Both registration scopes
+# are read (#2499): user scope, then the nearest-ancestor project scope.
 _GBRAIN_MCP_MODE="none"
+_GBRAIN_MCP_ENTRY=""
 if command -v jq >/dev/null 2>&1 && [ -f "$HOME/.claude.json" ]; then
-  _GBRAIN_MCP_TYPE=$(jq -r '.mcpServers.gbrain.type // .mcpServers.gbrain.transport // empty' "$HOME/.claude.json" 2>/dev/null)
+  _GBRAIN_MCP_ENTRY=$(jq -c --arg cwd "$PWD" '.mcpServers.gbrain // ((.projects // {}) | to_entries | map(select((.key as $k | $cwd == $k or ($cwd | startswith($k + "/"))) and ((try .value.mcpServers.gbrain catch null) != null))) | sort_by(.key | length) | last | .value.mcpServers.gbrain) // empty' "$HOME/.claude.json" 2>/dev/null)
+  _GBRAIN_MCP_TYPE=$(printf '%s' "$_GBRAIN_MCP_ENTRY" | jq -r '.type // .transport // empty' 2>/dev/null)
   case "$_GBRAIN_MCP_TYPE" in
     url|http|sse) _GBRAIN_MCP_MODE="remote-http" ;;
     stdio) _GBRAIN_MCP_MODE="local-stdio" ;;
@@ -419,7 +422,7 @@ fi
 if [ "$_GBRAIN_MCP_MODE" = "remote-http" ]; then
   # Remote-MCP mode: local artifacts sync is a no-op (brain admin's server
   # pulls from GitHub/GitLab). Show the user this is by design, not broken.
-  _GBRAIN_HOST=$(jq -r '.mcpServers.gbrain.url // empty' "$HOME/.claude.json" 2>/dev/null | sed -E 's|^https?://([^/:]+).*|\1|' | head -1 | tr -cd 'A-Za-z0-9._-')
+  _GBRAIN_HOST=$(printf '%s' "${_GBRAIN_MCP_ENTRY:-}" | jq -r '.url // empty' 2>/dev/null | sed -E 's|^https?://([^/:]+).*|\1|' | head -1 | tr -cd 'A-Za-z0-9._-')
   echo "ARTIFACTS_SYNC: remote-mode (managed by brain server ${_GBRAIN_HOST:-remote})"
 elif [ -d "$_GSTACK_HOME/.git" ] && [ "$_BRAIN_SYNC_MODE" != "off" ]; then
   _BRAIN_QUEUE_DEPTH=0
diff --git a/bin/gstack-brain-cache b/bin/gstack-brain-cache
index 301483632..abf45a013 100755
--- a/bin/gstack-brain-cache
+++ b/bin/gstack-brain-cache
@@ -126,13 +126,27 @@ function sha8(input: string): string {
  * Detects the active brain endpoint (MCP URL or 'local') and returns its
  * stable identity hash. Used to detect when the user switches brains
  * (different endpoint → different cache).
+ *
+ * Reads BOTH registration scopes in ~/.claude.json (#2499): user scope
+ * (.mcpServers.gbrain) first, then project scope
+ * (.projects["/abs/path"].mcpServers.gbrain — what `claude mcp add`
+ * WITHOUT --scope user writes), preferring the nearest ancestor of cwd
+ * (longest matching project key) so nested repos resolve to their own
+ * brain. Before the project-scope read, two different project-scoped
+ * brains both hashed to 'local', so switching between them never
+ * invalidated the cache — the exact scenario this function exists to
+ * catch.
+ *
+ * Params exist for tests; production callers use the defaults.
  */
-export function detectEndpointHash(): string {
-  const claudeJsonPath = join(homedir(), '.claude.json');
+export function detectEndpointHash(
+  claudeJsonPath: string = join(homedir(), '.claude.json'),
+  cwd: string = process.cwd(),
+): string {
   if (existsSync(claudeJsonPath)) {
     try {
       const cfg = JSON.parse(readFileSync(claudeJsonPath, 'utf-8'));
-      const gbrainServer = cfg?.mcpServers?.gbrain;
+      const gbrainServer = resolveGbrainMcpEntry(cfg, cwd);
       const url = gbrainServer?.url || gbrainServer?.transport?.url;
       if (typeof url === 'string' && url.length > 0) {
         return sha8(url);
@@ -143,6 +157,40 @@ export function detectEndpointHash(): string {
   return 'local';
 }
 
+interface McpEntryish {
+  url?: unknown;
+  transport?: { url?: unknown };
+}
+
+/**
+ * User-scope gbrain entry, else the nearest-ancestor project-scope entry
+ * for cwd (#2499). Path-boundary-aware: /a/repo never matches /a/repo2.
+ * Both separators are accepted so Windows project keys resolve.
+ */
+function resolveGbrainMcpEntry(
+  cfg: unknown,
+  cwd: string,
+): McpEntryish | undefined {
+  const root = cfg as {
+    mcpServers?: Record<string, McpEntryish>;
+    projects?: Record<string, { mcpServers?: Record<string, McpEntryish> }>;
+  } | null;
+  if (root?.mcpServers?.gbrain) return root.mcpServers.gbrain;
+  const projects = root?.projects;
+  if (!projects || typeof projects !== 'object') return undefined;
+  let best: { key: string; entry: McpEntryish } | undefined;
+  for (const [key, val] of Object.entries(projects)) {
+    if (!val || typeof val !== 'object') continue;
+    const entry = val.mcpServers?.gbrain;
+    if (!entry || typeof entry !== 'object') continue;
+    const isAncestor =
+      cwd === key || cwd.startsWith(`${key}/`) || cwd.startsWith(`${key}\\`);
+    if (!isAncestor) continue;
+    if (!best || key.length > best.key.length) best = { key, entry };
+  }
+  return best?.entry;
+}
+
 // ──────────────────────────────────────────────────────────────────────────
 // Atomic write (tmp + rename)
 // ──────────────────────────────────────────────────────────────────────────
diff --git a/browse/SKILL.md b/browse/SKILL.md
index 5e06c5b39..37b6b1a19 100644
--- a/browse/SKILL.md
+++ b/browse/SKILL.md
@@ -379,10 +379,13 @@ _BRAIN_SYNC_MODE=$("$_BRAIN_CONFIG_BIN" get artifacts_sync_mode 2>/dev/null || e
 # Detect remote-MCP mode (Path 4 of /setup-gbrain). Local artifacts sync is
 # a no-op in remote mode; the brain server pulls from GitHub/GitLab on its
 # own cadence. Read claude.json directly to keep this preamble fast (no
-# subprocess to claude CLI on every skill start).
+# subprocess to claude CLI on every skill start). Both registration scopes
+# are read (#2499): user scope, then the nearest-ancestor project scope.
 _GBRAIN_MCP_MODE="none"
+_GBRAIN_MCP_ENTRY=""
 if command -v jq >/dev/null 2>&1 && [ -f "$HOME/.claude.json" ]; then
-  _GBRAIN_MCP_TYPE=$(jq -r '.mcpServers.gbrain.type // .mcpServers.gbrain.transport // empty' "$HOME/.claude.json" 2>/dev/null)
+  _GBRAIN_MCP_ENTRY=$(jq -c --arg cwd "$PWD" '.mcpServers.gbrain // ((.projects // {}) | to_entries | map(select((.key as $k | $cwd == $k or ($cwd | startswith($k + "/"))) and ((try .value.mcpServers.gbrain catch null) != null))) | sort_by(.key | length) | last | .value.mcpServers.gbrain) // empty' "$HOME/.claude.json" 2>/dev/null)
+  _GBRAIN_MCP_TYPE=$(printf '%s' "$_GBRAIN_MCP_ENTRY" | jq -r '.type // .transport // empty' 2>/dev/null)
   case "$_GBRAIN_MCP_TYPE" in
     url|http|sse) _GBRAIN_MCP_MODE="remote-http" ;;
     stdio) _GBRAIN_MCP_MODE="local-stdio" ;;
@@ -417,7 +420,7 @@ fi
 if [ "$_GBRAIN_MCP_MODE" = "remote-http" ]; then
   # Remote-MCP mode: local artifacts sync is a no-op (brain admin's server
   # pulls from GitHub/GitLab). Show the user this is by design, not broken.
-  _GBRAIN_HOST=$(jq -r '.mcpServers.gbrain.url // empty' "$HOME/.claude.json" 2>/dev/null | sed -E 's|^https?://([^/:]+).*|\1|' | head -1 | tr -cd 'A-Za-z0-9._-')
+  _GBRAIN_HOST=$(printf '%s' "${_GBRAIN_MCP_ENTRY:-}" | jq -r '.url // empty' 2>/dev/null | sed -E 's|^https?://([^/:]+).*|\1|' | head -1 | tr -cd 'A-Za-z0-9._-')
   echo "ARTIFACTS_SYNC: remote-mode (managed by brain server ${_GBRAIN_HOST:-remote})"
 elif [ -d "$_GSTACK_HOME/.git" ] && [ "$_BRAIN_SYNC_MODE" != "off" ]; then
   _BRAIN_QUEUE_DEPTH=0
diff --git a/canary/SKILL.md b/canary/SKILL.md
index 5a2e02158..806e1f3b9 100644
--- a/canary/SKILL.md
+++ b/canary/SKILL.md
@@ -504,10 +504,13 @@ _BRAIN_SYNC_MODE=$("$_BRAIN_CONFIG_BIN" get artifacts_sync_mode 2>/dev/null || e
 # Detect remote-MCP mode (Path 4 of /setup-gbrain). Local artifacts sync is
 # a no-op in remote mode; the brain server pulls from GitHub/GitLab on its
 # own cadence. Read claude.json directly to keep this preamble fast (no
-# subprocess to claude CLI on every skill start).
+# subprocess to claude CLI on every skill start). Both registration scopes
+# are read (#2499): user scope, then the nearest-ancestor project scope.
 _GBRAIN_MCP_MODE="none"
+_GBRAIN_MCP_ENTRY=""
 if command -v jq >/dev/null 2>&1 && [ -f "$HOME/.claude.json" ]; then
-  _GBRAIN_MCP_TYPE=$(jq -r '.mcpServers.gbrain.type // .mcpServers.gbrain.transport // empty' "$HOME/.claude.json" 2>/dev/null)
+  _GBRAIN_MCP_ENTRY=$(jq -c --arg cwd "$PWD" '.mcpServers.gbrain // ((.projects // {}) | to_entries | map(select((.key as $k | $cwd == $k or ($cwd | startswith($k + "/"))) and ((try .value.mcpServers.gbrain catch null) != null))) | sort_by(.key | length) | last | .value.mcpServers.gbrain) // empty' "$HOME/.claude.json" 2>/dev/null)
+  _GBRAIN_MCP_TYPE=$(printf '%s' "$_GBRAIN_MCP_ENTRY" | jq -r '.type // .transport // empty' 2>/dev/null)
   case "$_GBRAIN_MCP_TYPE" in
     url|http|sse) _GBRAIN_MCP_MODE="remote-http" ;;
     stdio) _GBRAIN_MCP_MODE="local-stdio" ;;
@@ -542,7 +545,7 @@ fi
 if [ "$_GBRAIN_MCP_MODE" = "remote-http" ]; then
   # Remote-MCP mode: local artifacts sync is a no-op (brain admin's server
   # pulls from GitHub/GitLab). Show the user this is by design, not broken.
-  _GBRAIN_HOST=$(jq -r '.mcpServers.gbrain.url // empty' "$HOME/.claude.json" 2>/dev/null | sed -E 's|^https?://([^/:]+).*|\1|' | head -1 | tr -cd 'A-Za-z0-9._-')
+  _GBRAIN_HOST=$(printf '%s' "${_GBRAIN_MCP_ENTRY:-}" | jq -r '.url // empty' 2>/dev/null | sed -E 's|^https?://([^/:]+).*|\1|' | head -1 | tr -cd 'A-Za-z0-9._-')
   echo "ARTIFACTS_SYNC: remote-mode (managed by brain server ${_GBRAIN_HOST:-remote})"
 elif [ -d "$_GSTACK_HOME/.git" ] && [ "$_BRAIN_SYNC_MODE" != "off" ]; then
   _BRAIN_QUEUE_DEPTH=0
diff --git a/codex/SKILL.md b/codex/SKILL.md
index 4470be50d..36eadff5e 100644
--- a/codex/SKILL.md
+++ b/codex/SKILL.md
@@ -507,10 +507,13 @@ _BRAIN_SYNC_MODE=$("$_BRAIN_CONFIG_BIN" get artifacts_sync_mode 2>/dev/null || e
 # Detect remote-MCP mode (Path 4 of /setup-gbrain). Local artifacts sync is
 # a no-op in remote mode; the brain server pulls from GitHub/GitLab on its
 # own cadence. Read claude.json directly to keep this preamble fast (no
-# subprocess to claude CLI on every skill start).
+# subprocess to claude CLI on every skill start). Both registration scopes
+# are read (#2499): user scope, then the nearest-ancestor project scope.
 _GBRAIN_MCP_MODE="none"
+_GBRAIN_MCP_ENTRY=""
 if command -v jq >/dev/null 2>&1 && [ -f "$HOME/.claude.json" ]; then
-  _GBRAIN_MCP_TYPE=$(jq -r '.mcpServers.gbrain.type // .mcpServers.gbrain.transport // empty' "$HOME/.claude.json" 2>/dev/null)
+  _GBRAIN_MCP_ENTRY=$(jq -c --arg cwd "$PWD" '.mcpServers.gbrain // ((.projects // {}) | to_entries | map(select((.key as $k | $cwd == $k or ($cwd | startswith($k + "/"))) and ((try .value.mcpServers.gbrain catch null) != null))) | sort_by(.key | length) | last | .value.mcpServers.gbrain) // empty' "$HOME/.claude.json" 2>/dev/null)
+  _GBRAIN_MCP_TYPE=$(printf '%s' "$_GBRAIN_MCP_ENTRY" | jq -r '.type // .transport // empty' 2>/dev/null)
   case "$_GBRAIN_MCP_TYPE" in
     url|http|sse) _GBRAIN_MCP_MODE="remote-http" ;;
     stdio) _GBRAIN_MCP_MODE="local-stdio" ;;
@@ -545,7 +548,7 @@ fi
 if [ "$_GBRAIN_MCP_MODE" = "remote-http" ]; then
   # Remote-MCP mode: local artifacts sync is a no-op (brain admin's server
   # pulls from GitHub/GitLab). Show the user this is by design, not broken.
-  _GBRAIN_HOST=$(jq -r '.mcpServers.gbrain.url // empty' "$HOME/.claude.json" 2>/dev/null | sed -E 's|^https?://([^/:]+).*|\1|' | head -1 | tr -cd 'A-Za-z0-9._-')
+  _GBRAIN_HOST=$(printf '%s' "${_GBRAIN_MCP_ENTRY:-}" | jq -r '.url // empty' 2>/dev/null | sed -E 's|^https?://([^/:]+).*|\1|' | head -1 | tr -cd 'A-Za-z0-9._-')
   echo "ARTIFACTS_SYNC: remote-mode (managed by brain server ${_GBRAIN_HOST:-remote})"
 elif [ -d "$_GSTACK_HOME/.git" ] && [ "$_BRAIN_SYNC_MODE" != "off" ]; then
   _BRAIN_QUEUE_DEPTH=0
diff --git a/context-restore/SKILL.md b/context-restore/SKILL.md
index 0481d71fc..5a3c5b6ef 100644
--- a/context-restore/SKILL.md
+++ b/context-restore/SKILL.md
@@ -508,10 +508,13 @@ _BRAIN_SYNC_MODE=$("$_BRAIN_CONFIG_BIN" get artifacts_sync_mode 2>/dev/null || e
 # Detect remote-MCP mode (Path 4 of /setup-gbrain). Local artifacts sync is
 # a no-op in remote mode; the brain server pulls from GitHub/GitLab on its
 # own cadence. Read claude.json directly to keep this preamble fast (no
-# subprocess to claude CLI on every skill start).
+# subprocess to claude CLI on every skill start). Both registration scopes
+# are read (#2499): user scope, then the nearest-ancestor project scope.
 _GBRAIN_MCP_MODE="none"
+_GBRAIN_MCP_ENTRY=""
 if command -v jq >/dev/null 2>&1 && [ -f "$HOME/.claude.json" ]; then
-  _GBRAIN_MCP_TYPE=$(jq -r '.mcpServers.gbrain.type // .mcpServers.gbrain.transport // empty' "$HOME/.claude.json" 2>/dev/null)
+  _GBRAIN_MCP_ENTRY=$(jq -c --arg cwd "$PWD" '.mcpServers.gbrain // ((.projects // {}) | to_entries | map(select((.key as $k | $cwd == $k or ($cwd | startswith($k + "/"))) and ((try .value.mcpServers.gbrain catch null) != null))) | sort_by(.key | length) | last | .value.mcpServers.gbrain) // empty' "$HOME/.claude.json" 2>/dev/null)
+  _GBRAIN_MCP_TYPE=$(printf '%s' "$_GBRAIN_MCP_ENTRY" | jq -r '.type // .transport // empty' 2>/dev/null)
   case "$_GBRAIN_MCP_TYPE" in
     url|http|sse) _GBRAIN_MCP_MODE="remote-http" ;;
     stdio) _GBRAIN_MCP_MODE="local-stdio" ;;
@@ -546,7 +549,7 @@ fi
 if [ "$_GBRAIN_MCP_MODE" = "remote-http" ]; then
   # Remote-MCP mode: local artifacts sync is a no-op (brain admin's server
   # pulls from GitHub/GitLab). Show the user this is by design, not broken.
-  _GBRAIN_HOST=$(jq -r '.mcpServers.gbrain.url // empty' "$HOME/.claude.json" 2>/dev/null | sed -E 's|^https?://([^/:]+).*|\1|' | head -1 | tr -cd 'A-Za-z0-9._-')
+  _GBRAIN_HOST=$(printf '%s' "${_GBRAIN_MCP_ENTRY:-}" | jq -r '.url // empty' 2>/dev/null | sed -E 's|^https?://([^/:]+).*|\1|' | head -1 | tr -cd 'A-Za-z0-9._-')
   echo "ARTIFACTS_SYNC: remote-mode (managed by brain server ${_GBRAIN_HOST:-remote})"
 elif [ -d "$_GSTACK_HOME/.git" ] && [ "$_BRAIN_SYNC_MODE" != "off" ]; then
   _BRAIN_QUEUE_DEPTH=0
diff --git a/context-save/SKILL.md b/context-save/SKILL.md
index 02d3db51b..be9df4146 100644
--- a/context-save/SKILL.md
+++ b/context-save/SKILL.md
@@ -507,10 +507,13 @@ _BRAIN_SYNC_MODE=$("$_BRAIN_CONFIG_BIN" get artifacts_sync_mode 2>/dev/null || e
 # Detect remote-MCP mode (Path 4 of /setup-gbrain). Local artifacts sync is
 # a no-op in remote mode; the brain server pulls from GitHub/GitLab on its
 # own cadence. Read claude.json directly to keep this preamble fast (no
-# subprocess to claude CLI on every skill start).
+# subprocess to claude CLI on every skill start). Both registration scopes
+# are read (#2499): user scope, then the nearest-ancestor project scope.
 _GBRAIN_MCP_MODE="none"
+_GBRAIN_MCP_ENTRY=""
 if command -v jq >/dev/null 2>&1 && [ -f "$HOME/.claude.json" ]; then
-  _GBRAIN_MCP_TYPE=$(jq -r '.mcpServers.gbrain.type // .mcpServers.gbrain.transport // empty' "$HOME/.claude.json" 2>/dev/null)
+  _GBRAIN_MCP_ENTRY=$(jq -c --arg cwd "$PWD" '.mcpServers.gbrain // ((.projects // {}) | to_entries | map(select((.key as $k | $cwd == $k or ($cwd | startswith($k + "/"))) and ((try .value.mcpServers.gbrain catch null) != null))) | sort_by(.key | length) | last | .value.mcpServers.gbrain) // empty' "$HOME/.claude.json" 2>/dev/null)
+  _GBRAIN_MCP_TYPE=$(printf '%s' "$_GBRAIN_MCP_ENTRY" | jq -r '.type // .transport // empty' 2>/dev/null)
   case "$_GBRAIN_MCP_TYPE" in
     url|http|sse) _GBRAIN_MCP_MODE="remote-http" ;;
     stdio) _GBRAIN_MCP_MODE="local-stdio" ;;
@@ -545,7 +548,7 @@ fi
 if [ "$_GBRAIN_MCP_MODE" = "remote-http" ]; then
   # Remote-MCP mode: local artifacts sync is a no-op (brain admin's server
   # pulls from GitHub/GitLab). Show the user this is by design, not broken.
-  _GBRAIN_HOST=$(jq -r '.mcpServers.gbrain.url // empty' "$HOME/.claude.json" 2>/dev/null | sed -E 's|^https?://([^/:]+).*|\1|' | head -1 | tr -cd 'A-Za-z0-9._-')
+  _GBRAIN_HOST=$(printf '%s' "${_GBRAIN_MCP_ENTRY:-}" | jq -r '.url // empty' 2>/dev/null | sed -E 's|^https?://([^/:]+).*|\1|' | head -1 | tr -cd 'A-Za-z0-9._-')
   echo "ARTIFACTS_SYNC: remote-mode (managed by brain server ${_GBRAIN_HOST:-remote})"
 elif [ -d "$_GSTACK_HOME/.git" ] && [ "$_BRAIN_SYNC_MODE" != "off" ]; then
   _BRAIN_QUEUE_DEPTH=0
diff --git a/cso/SKILL.md b/cso/SKILL.md
index 06c4b37cf..99e6cb9c0 100644
--- a/cso/SKILL.md
+++ b/cso/SKILL.md
@@ -510,10 +510,13 @@ _BRAIN_SYNC_MODE=$("$_BRAIN_CONFIG_BIN" get artifacts_sync_mode 2>/dev/null || e
 # Detect remote-MCP mode (Path 4 of /setup-gbrain). Local artifacts sync is
 # a no-op in remote mode; the brain server pulls from GitHub/GitLab on its
 # own cadence. Read claude.json directly to keep this preamble fast (no
-# subprocess to claude CLI on every skill start).
+# subprocess to claude CLI on every skill start). Both registration scopes
+# are read (#2499): user scope, then the nearest-ancestor project scope.
 _GBRAIN_MCP_MODE="none"
+_GBRAIN_MCP_ENTRY=""
 if command -v jq >/dev/null 2>&1 && [ -f "$HOME/.claude.json" ]; then
-  _GBRAIN_MCP_TYPE=$(jq -r '.mcpServers.gbrain.type // .mcpServers.gbrain.transport // empty' "$HOME/.claude.json" 2>/dev/null)
+  _GBRAIN_MCP_ENTRY=$(jq -c --arg cwd "$PWD" '.mcpServers.gbrain // ((.projects // {}) | to_entries | map(select((.key as $k | $cwd == $k or ($cwd | startswith($k + "/"))) and ((try .value.mcpServers.gbrain catch null) != null))) | sort_by(.key | length) | last | .value.mcpServers.gbrain) // empty' "$HOME/.claude.json" 2>/dev/null)
+  _GBRAIN_MCP_TYPE=$(printf '%s' "$_GBRAIN_MCP_ENTRY" | jq -r '.type // .transport // empty' 2>/dev/null)
   case "$_GBRAIN_MCP_TYPE" in
     url|http|sse) _GBRAIN_MCP_MODE="remote-http" ;;
     stdio) _GBRAIN_MCP_MODE="local-stdio" ;;
@@ -548,7 +551,7 @@ fi
 if [ "$_GBRAIN_MCP_MODE" = "remote-http" ]; then
   # Remote-MCP mode: local artifacts sync is a no-op (brain admin's server
   # pulls from GitHub/GitLab). Show the user this is by design, not broken.
-  _GBRAIN_HOST=$(jq -r '.mcpServers.gbrain.url // empty' "$HOME/.claude.json" 2>/dev/null | sed -E 's|^https?://([^/:]+).*|\1|' | head -1 | tr -cd 'A-Za-z0-9._-')
+  _GBRAIN_HOST=$(printf '%s' "${_GBRAIN_MCP_ENTRY:-}" | jq -r '.url // empty' 2>/dev/null | sed -E 's|^https?://([^/:]+).*|\1|' | head -1 | tr -cd 'A-Za-z0-9._-')
   echo "ARTIFACTS_SYNC: remote-mode (managed by brain server ${_GBRAIN_HOST:-remote})"
 elif [ -d "$_GSTACK_HOME/.git" ] && [ "$_BRAIN_SYNC_MODE" != "off" ]; then
   _BRAIN_QUEUE_DEPTH=0
diff --git a/design-consultation/SKILL.md b/design-consultation/SKILL.md
index c7c248aca..57450909c 100644
--- a/design-consultation/SKILL.md
+++ b/design-consultation/SKILL.md
@@ -530,10 +530,13 @@ _BRAIN_SYNC_MODE=$("$_BRAIN_CONFIG_BIN" get artifacts_sync_mode 2>/dev/null || e
 # Detect remote-MCP mode (Path 4 of /setup-gbrain). Local artifacts sync is
 # a no-op in remote mode; the brain server pulls from GitHub/GitLab on its
 # own cadence. Read claude.json directly to keep this preamble fast (no
-# subprocess to claude CLI on every skill start).
+# subprocess to claude CLI on every skill start). Both registration scopes
+# are read (#2499): user scope, then the nearest-ancestor project scope.
 _GBRAIN_MCP_MODE="none"
+_GBRAIN_MCP_ENTRY=""
 if command -v jq >/dev/null 2>&1 && [ -f "$HOME/.claude.json" ]; then
-  _GBRAIN_MCP_TYPE=$(jq -r '.mcpServers.gbrain.type // .mcpServers.gbrain.transport // empty' "$HOME/.claude.json" 2>/dev/null)
+  _GBRAIN_MCP_ENTRY=$(jq -c --arg cwd "$PWD" '.mcpServers.gbrain // ((.projects // {}) | to_entries | map(select((.key as $k | $cwd == $k or ($cwd | startswith($k + "/"))) and ((try .value.mcpServers.gbrain catch null) != null))) | sort_by(.key | length) | last | .value.mcpServers.gbrain) // empty' "$HOME/.claude.json" 2>/dev/null)
+  _GBRAIN_MCP_TYPE=$(printf '%s' "$_GBRAIN_MCP_ENTRY" | jq -r '.type // .transport // empty' 2>/dev/null)
   case "$_GBRAIN_MCP_TYPE" in
     url|http|sse) _GBRAIN_MCP_MODE="remote-http" ;;
     stdio) _GBRAIN_MCP_MODE="local-stdio" ;;
@@ -568,7 +571,7 @@ fi
 if [ "$_GBRAIN_MCP_MODE" = "remote-http" ]; then
   # Remote-MCP mode: local artifacts sync is a no-op (brain admin's server
   # pulls from GitHub/GitLab). Show the user this is by design, not broken.
-  _GBRAIN_HOST=$(jq -r '.mcpServers.gbrain.url // empty' "$HOME/.claude.json" 2>/dev/null | sed -E 's|^https?://([^/:]+).*|\1|' | head -1 | tr -cd 'A-Za-z0-9._-')
+  _GBRAIN_HOST=$(printf '%s' "${_GBRAIN_MCP_ENTRY:-}" | jq -r '.url // empty' 2>/dev/null | sed -E 's|^https?://([^/:]+).*|\1|' | head -1 | tr -cd 'A-Za-z0-9._-')
   echo "ARTIFACTS_SYNC: remote-mode (managed by brain server ${_GBRAIN_HOST:-remote})"
 elif [ -d "$_GSTACK_HOME/.git" ] && [ "$_BRAIN_SYNC_MODE" != "off" ]; then
   _BRAIN_QUEUE_DEPTH=0
diff --git a/design-html/SKILL.md b/design-html/SKILL.md
index 742358e34..a9e1ac1a9 100644
--- a/design-html/SKILL.md
+++ b/design-html/SKILL.md
@@ -511,10 +511,13 @@ _BRAIN_SYNC_MODE=$("$_BRAIN_CONFIG_BIN" get artifacts_sync_mode 2>/dev/null || e
 # Detect remote-MCP mode (Path 4 of /setup-gbrain). Local artifacts sync is
 # a no-op in remote mode; the brain server pulls from GitHub/GitLab on its
 # own cadence. Read claude.json directly to keep this preamble fast (no
-# subprocess to claude CLI on every skill start).
+# subprocess to claude CLI on every skill start). Both registration scopes
+# are read (#2499): user scope, then the nearest-ancestor project scope.
 _GBRAIN_MCP_MODE="none"
+_GBRAIN_MCP_ENTRY=""
 if command -v jq >/dev/null 2>&1 && [ -f "$HOME/.claude.json" ]; then
-  _GBRAIN_MCP_TYPE=$(jq -r '.mcpServers.gbrain.type // .mcpServers.gbrain.transport // empty' "$HOME/.claude.json" 2>/dev/null)
+  _GBRAIN_MCP_ENTRY=$(jq -c --arg cwd "$PWD" '.mcpServers.gbrain // ((.projects // {}) | to_entries | map(select((.key as $k | $cwd == $k or ($cwd | startswith($k + "/"))) and ((try .value.mcpServers.gbrain catch null) != null))) | sort_by(.key | length) | last | .value.mcpServers.gbrain) // empty' "$HOME/.claude.json" 2>/dev/null)
+  _GBRAIN_MCP_TYPE=$(printf '%s' "$_GBRAIN_MCP_ENTRY" | jq -r '.type // .transport // empty' 2>/dev/null)
   case "$_GBRAIN_MCP_TYPE" in
     url|http|sse) _GBRAIN_MCP_MODE="remote-http" ;;
     stdio) _GBRAIN_MCP_MODE="local-stdio" ;;
@@ -549,7 +552,7 @@ fi
 if [ "$_GBRAIN_MCP_MODE" = "remote-http" ]; then
   # Remote-MCP mode: local artifacts sync is a no-op (brain admin's server
   # pulls from GitHub/GitLab). Show the user this is by design, not broken.
-  _GBRAIN_HOST=$(jq -r '.mcpServers.gbrain.url // empty' "$HOME/.claude.json" 2>/dev/null | sed -E 's|^https?://([^/:]+).*|\1|' | head -1 | tr -cd 'A-Za-z0-9._-')
+  _GBRAIN_HOST=$(printf '%s' "${_GBRAIN_MCP_ENTRY:-}" | jq -r '.url // empty' 2>/dev/null | sed -E 's|^https?://([^/:]+).*|\1|' | head -1 | tr -cd 'A-Za-z0-9._-')
   echo "ARTIFACTS_SYNC: remote-mode (managed by brain server ${_GBRAIN_HOST:-remote})"
 elif [ -d "$_GSTACK_HOME/.git" ] && [ "$_BRAIN_SYNC_MODE" != "off" ]; then
   _BRAIN_QUEUE_DEPTH=0
diff --git a/design-review/SKILL.md b/design-review/SKILL.md
index efd98527f..786423e76 100644
--- a/design-review/SKILL.md
+++ b/design-review/SKILL.md
@@ -508,10 +508,13 @@ _BRAIN_SYNC_MODE=$("$_BRAIN_CONFIG_BIN" get artifacts_sync_mode 2>/dev/null || e
 # Detect remote-MCP mode (Path 4 of /setup-gbrain). Local artifacts sync is
 # a no-op in remote mode; the brain server pulls from GitHub/GitLab on its
 # own cadence. Read claude.json directly to keep this preamble fast (no
-# subprocess to claude CLI on every skill start).
+# subprocess to claude CLI on every skill start). Both registration scopes
+# are read (#2499): user scope, then the nearest-ancestor project scope.
 _GBRAIN_MCP_MODE="none"
+_GBRAIN_MCP_ENTRY=""
 if command -v jq >/dev/null 2>&1 && [ -f "$HOME/.claude.json" ]; then
-  _GBRAIN_MCP_TYPE=$(jq -r '.mcpServers.gbrain.type // .mcpServers.gbrain.transport // empty' "$HOME/.claude.json" 2>/dev/null)
+  _GBRAIN_MCP_ENTRY=$(jq -c --arg cwd "$PWD" '.mcpServers.gbrain // ((.projects // {}) | to_entries | map(select((.key as $k | $cwd == $k or ($cwd | startswith($k + "/"))) and ((try .value.mcpServers.gbrain catch null) != null))) | sort_by(.key | length) | last | .value.mcpServers.gbrain) // empty' "$HOME/.claude.json" 2>/dev/null)
+  _GBRAIN_MCP_TYPE=$(printf '%s' "$_GBRAIN_MCP_ENTRY" | jq -r '.type // .transport // empty' 2>/dev/null)
   case "$_GBRAIN_MCP_TYPE" in
     url|http|sse) _GBRAIN_MCP_MODE="remote-http" ;;
     stdio) _GBRAIN_MCP_MODE="local-stdio" ;;
@@ -546,7 +549,7 @@ fi
 if [ "$_GBRAIN_MCP_MODE" = "remote-http" ]; then
   # Remote-MCP mode: local artifacts sync is a no-op (brain admin's server
   # pulls from GitHub/GitLab). Show the user this is by design, not broken.
-  _GBRAIN_HOST=$(jq -r '.mcpServers.gbrain.url // empty' "$HOME/.claude.json" 2>/dev/null | sed -E 's|^https?://([^/:]+).*|\1|' | head -1 | tr -cd 'A-Za-z0-9._-')
+  _GBRAIN_HOST=$(printf '%s' "${_GBRAIN_MCP_ENTRY:-}" | jq -r '.url // empty' 2>/dev/null | sed -E 's|^https?://([^/:]+).*|\1|' | head -1 | tr -cd 'A-Za-z0-9._-')
   echo "ARTIFACTS_SYNC: remote-mode (managed by brain server ${_GBRAIN_HOST:-remote})"
 elif [ -d "$_GSTACK_HOME/.git" ] && [ "$_BRAIN_SYNC_MODE" != "off" ]; then
   _BRAIN_QUEUE_DEPTH=0
diff --git a/design-shotgun/SKILL.md b/design-shotgun/SKILL.md
index f2fc831bf..4066154c1 100644
--- a/design-shotgun/SKILL.md
+++ b/design-shotgun/SKILL.md
@@ -525,10 +525,13 @@ _BRAIN_SYNC_MODE=$("$_BRAIN_CONFIG_BIN" get artifacts_sync_mode 2>/dev/null || e
 # Detect remote-MCP mode (Path 4 of /setup-gbrain). Local artifacts sync is
 # a no-op in remote mode; the brain server pulls from GitHub/GitLab on its
 # own cadence. Read claude.json directly to keep this preamble fast (no
-# subprocess to claude CLI on every skill start).
+# subprocess to claude CLI on every skill start). Both registration scopes
+# are read (#2499): user scope, then the nearest-ancestor project scope.
 _GBRAIN_MCP_MODE="none"
+_GBRAIN_MCP_ENTRY=""
 if command -v jq >/dev/null 2>&1 && [ -f "$HOME/.claude.json" ]; then
-  _GBRAIN_MCP_TYPE=$(jq -r '.mcpServers.gbrain.type // .mcpServers.gbrain.transport // empty' "$HOME/.claude.json" 2>/dev/null)
+  _GBRAIN_MCP_ENTRY=$(jq -c --arg cwd "$PWD" '.mcpServers.gbrain // ((.projects // {}) | to_entries | map(select((.key as $k | $cwd == $k or ($cwd | startswith($k + "/"))) and ((try .value.mcpServers.gbrain catch null) != null))) | sort_by(.key | length) | last | .value.mcpServers.gbrain) // empty' "$HOME/.claude.json" 2>/dev/null)
+  _GBRAIN_MCP_TYPE=$(printf '%s' "$_GBRAIN_MCP_ENTRY" | jq -r '.type // .transport // empty' 2>/dev/null)
   case "$_GBRAIN_MCP_TYPE" in
     url|http|sse) _GBRAIN_MCP_MODE="remote-http" ;;
     stdio) _GBRAIN_MCP_MODE="local-stdio" ;;
@@ -563,7 +566,7 @@ fi
 if [ "$_GBRAIN_MCP_MODE" = "remote-http" ]; then
   # Remote-MCP mode: local artifacts sync is a no-op (brain admin's server
   # pulls from GitHub/GitLab). Show the user this is by design, not broken.
-  _GBRAIN_HOST=$(jq -r '.mcpServers.gbrain.url // empty' "$HOME/.claude.json" 2>/dev/null | sed -E 's|^https?://([^/:]+).*|\1|' | head -1 | tr -cd 'A-Za-z0-9._-')
+  _GBRAIN_HOST=$(printf '%s' "${_GBRAIN_MCP_ENTRY:-}" | jq -r '.url // empty' 2>/dev/null | sed -E 's|^https?://([^/:]+).*|\1|' | head -1 | tr -cd 'A-Za-z0-9._-')
   echo "ARTIFACTS_SYNC: remote-mode (managed by brain server ${_GBRAIN_HOST:-remote})"
 elif [ -d "$_GSTACK_HOME/.git" ] && [ "$_BRAIN_SYNC_MODE" != "off" ]; then
   _BRAIN_QUEUE_DEPTH=0
diff --git a/devex-review/SKILL.md b/devex-review/SKILL.md
index 571816f7d..1450b9bbb 100644
--- a/devex-review/SKILL.md
+++ b/devex-review/SKILL.md
@@ -510,10 +510,13 @@ _BRAIN_SYNC_MODE=$("$_BRAIN_CONFIG_BIN" get artifacts_sync_mode 2>/dev/null || e
 # Detect remote-MCP mode (Path 4 of /setup-gbrain). Local artifacts sync is
 # a no-op in remote mode; the brain server pulls from GitHub/GitLab on its
 # own cadence. Read claude.json directly to keep this preamble fast (no
-# subprocess to claude CLI on every skill start).
+# subprocess to claude CLI on every skill start). Both registration scopes
+# are read (#2499): user scope, then the nearest-ancestor project scope.
 _GBRAIN_MCP_MODE="none"
+_GBRAIN_MCP_ENTRY=""
 if command -v jq >/dev/null 2>&1 && [ -f "$HOME/.claude.json" ]; then
-  _GBRAIN_MCP_TYPE=$(jq -r '.mcpServers.gbrain.type // .mcpServers.gbrain.transport // empty' "$HOME/.claude.json" 2>/dev/null)
+  _GBRAIN_MCP_ENTRY=$(jq -c --arg cwd "$PWD" '.mcpServers.gbrain // ((.projects // {}) | to_entries | map(select((.key as $k | $cwd == $k or ($cwd | startswith($k + "/"))) and ((try .value.mcpServers.gbrain catch null) != null))) | sort_by(.key | length) | last | .value.mcpServers.gbrain) // empty' "$HOME/.claude.json" 2>/dev/null)
+  _GBRAIN_MCP_TYPE=$(printf '%s' "$_GBRAIN_MCP_ENTRY" | jq -r '.type // .transport // empty' 2>/dev/null)
   case "$_GBRAIN_MCP_TYPE" in
     url|http|sse) _GBRAIN_MCP_MODE="remote-http" ;;
     stdio) _GBRAIN_MCP_MODE="local-stdio" ;;
@@ -548,7 +551,7 @@ fi
 if [ "$_GBRAIN_MCP_MODE" = "remote-http" ]; then
   # Remote-MCP mode: local artifacts sync is a no-op (brain admin's server
   # pulls from GitHub/GitLab). Show the user this is by design, not broken.
-  _GBRAIN_HOST=$(jq -r '.mcpServers.gbrain.url // empty' "$HOME/.claude.json" 2>/dev/null | sed -E 's|^https?://([^/:]+).*|\1|' | head -1 | tr -cd 'A-Za-z0-9._-')
+  _GBRAIN_HOST=$(printf '%s' "${_GBRAIN_MCP_ENTRY:-}" | jq -r '.url // empty' 2>/dev/null | sed -E 's|^https?://([^/:]+).*|\1|' | head -1 | tr -cd 'A-Za-z0-9._-')
   echo "ARTIFACTS_SYNC: remote-mode (managed by brain server ${_GBRAIN_HOST:-remote})"
 elif [ -d "$_GSTACK_HOME/.git" ] && [ "$_BRAIN_SYNC_MODE" != "off" ]; then
   _BRAIN_QUEUE_DEPTH=0
diff --git a/diagram/SKILL.md b/diagram/SKILL.md
index 0fc2de22d..c2d16b2fb 100644
--- a/diagram/SKILL.md
+++ b/diagram/SKILL.md
@@ -380,10 +380,13 @@ _BRAIN_SYNC_MODE=$("$_BRAIN_CONFIG_BIN" get artifacts_sync_mode 2>/dev/null || e
 # Detect remote-MCP mode (Path 4 of /setup-gbrain). Local artifacts sync is
 # a no-op in remote mode; the brain server pulls from GitHub/GitLab on its
 # own cadence. Read claude.json directly to keep this preamble fast (no
-# subprocess to claude CLI on every skill start).
+# subprocess to claude CLI on every skill start). Both registration scopes
+# are read (#2499): user scope, then the nearest-ancestor project scope.
 _GBRAIN_MCP_MODE="none"
+_GBRAIN_MCP_ENTRY=""
 if command -v jq >/dev/null 2>&1 && [ -f "$HOME/.claude.json" ]; then
-  _GBRAIN_MCP_TYPE=$(jq -r '.mcpServers.gbrain.type // .mcpServers.gbrain.transport // empty' "$HOME/.claude.json" 2>/dev/null)
+  _GBRAIN_MCP_ENTRY=$(jq -c --arg cwd "$PWD" '.mcpServers.gbrain // ((.projects // {}) | to_entries | map(select((.key as $k | $cwd == $k or ($cwd | startswith($k + "/"))) and ((try .value.mcpServers.gbrain catch null) != null))) | sort_by(.key | length) | last | .value.mcpServers.gbrain) // empty' "$HOME/.claude.json" 2>/dev/null)
+  _GBRAIN_MCP_TYPE=$(printf '%s' "$_GBRAIN_MCP_ENTRY" | jq -r '.type // .transport // empty' 2>/dev/null)
   case "$_GBRAIN_MCP_TYPE" in
     url|http|sse) _GBRAIN_MCP_MODE="remote-http" ;;
     stdio) _GBRAIN_MCP_MODE="local-stdio" ;;
@@ -418,7 +421,7 @@ fi
 if [ "$_GBRAIN_MCP_MODE" = "remote-http" ]; then
   # Remote-MCP mode: local artifacts sync is a no-op (brain admin's server
   # pulls from GitHub/GitLab). Show the user this is by design, not broken.
-  _GBRAIN_HOST=$(jq -r '.mcpServers.gbrain.url // empty' "$HOME/.claude.json" 2>/dev/null | sed -E 's|^https?://([^/:]+).*|\1|' | head -1 | tr -cd 'A-Za-z0-9._-')
+  _GBRAIN_HOST=$(printf '%s' "${_GBRAIN_MCP_ENTRY:-}" | jq -r '.url // empty' 2>/dev/null | sed -E 's|^https?://([^/:]+).*|\1|' | head -1 | tr -cd 'A-Za-z0-9._-')
   echo "ARTIFACTS_SYNC: remote-mode (managed by brain server ${_GBRAIN_HOST:-remote})"
 elif [ -d "$_GSTACK_HOME/.git" ] && [ "$_BRAIN_SYNC_MODE" != "off" ]; then
   _BRAIN_QUEUE_DEPTH=0
diff --git a/document-generate/SKILL.md b/document-generate/SKILL.md
index 3d7338c99..7d8b34bc0 100644
--- a/document-generate/SKILL.md
+++ b/document-generate/SKILL.md
@@ -510,10 +510,13 @@ _BRAIN_SYNC_MODE=$("$_BRAIN_CONFIG_BIN" get artifacts_sync_mode 2>/dev/null || e
 # Detect remote-MCP mode (Path 4 of /setup-gbrain). Local artifacts sync is
 # a no-op in remote mode; the brain server pulls from GitHub/GitLab on its
 # own cadence. Read claude.json directly to keep this preamble fast (no
-# subprocess to claude CLI on every skill start).
+# subprocess to claude CLI on every skill start). Both registration scopes
+# are read (#2499): user scope, then the nearest-ancestor project scope.
 _GBRAIN_MCP_MODE="none"
+_GBRAIN_MCP_ENTRY=""
 if command -v jq >/dev/null 2>&1 && [ -f "$HOME/.claude.json" ]; then
-  _GBRAIN_MCP_TYPE=$(jq -r '.mcpServers.gbrain.type // .mcpServers.gbrain.transport // empty' "$HOME/.claude.json" 2>/dev/null)
+  _GBRAIN_MCP_ENTRY=$(jq -c --arg cwd "$PWD" '.mcpServers.gbrain // ((.projects // {}) | to_entries | map(select((.key as $k | $cwd == $k or ($cwd | startswith($k + "/"))) and ((try .value.mcpServers.gbrain catch null) != null))) | sort_by(.key | length) | last | .value.mcpServers.gbrain) // empty' "$HOME/.claude.json" 2>/dev/null)
+  _GBRAIN_MCP_TYPE=$(printf '%s' "$_GBRAIN_MCP_ENTRY" | jq -r '.type // .transport // empty' 2>/dev/null)
   case "$_GBRAIN_MCP_TYPE" in
     url|http|sse) _GBRAIN_MCP_MODE="remote-http" ;;
     stdio) _GBRAIN_MCP_MODE="local-stdio" ;;
@@ -548,7 +551,7 @@ fi
 if [ "$_GBRAIN_MCP_MODE" = "remote-http" ]; then
   # Remote-MCP mode: local artifacts sync is a no-op (brain admin's server
   # pulls from GitHub/GitLab). Show the user this is by design, not broken.
-  _GBRAIN_HOST=$(jq -r '.mcpServers.gbrain.url // empty' "$HOME/.claude.json" 2>/dev/null | sed -E 's|^https?://([^/:]+).*|\1|' | head -1 | tr -cd 'A-Za-z0-9._-')
+  _GBRAIN_HOST=$(printf '%s' "${_GBRAIN_MCP_ENTRY:-}" | jq -r '.url // empty' 2>/dev/null | sed -E 's|^https?://([^/:]+).*|\1|' | head -1 | tr -cd 'A-Za-z0-9._-')
   echo "ARTIFACTS_SYNC: remote-mode (managed by brain server ${_GBRAIN_HOST:-remote})"
 elif [ -d "$_GSTACK_HOME/.git" ] && [ "$_BRAIN_SYNC_MODE" != "off" ]; then
   _BRAIN_QUEUE_DEPTH=0
diff --git a/document-release/SKILL.md b/document-release/SKILL.md
index e0a2b106e..a87ba0f18 100644
--- a/document-release/SKILL.md
+++ b/document-release/SKILL.md
@@ -508,10 +508,13 @@ _BRAIN_SYNC_MODE=$("$_BRAIN_CONFIG_BIN" get artifacts_sync_mode 2>/dev/null || e
 # Detect remote-MCP mode (Path 4 of /setup-gbrain). Local artifacts sync is
 # a no-op in remote mode; the brain server pulls from GitHub/GitLab on its
 # own cadence. Read claude.json directly to keep this preamble fast (no
-# subprocess to claude CLI on every skill start).
+# subprocess to claude CLI on every skill start). Both registration scopes
+# are read (#2499): user scope, then the nearest-ancestor project scope.
 _GBRAIN_MCP_MODE="none"
+_GBRAIN_MCP_ENTRY=""
 if command -v jq >/dev/null 2>&1 && [ -f "$HOME/.claude.json" ]; then
-  _GBRAIN_MCP_TYPE=$(jq -r '.mcpServers.gbrain.type // .mcpServers.gbrain.transport // empty' "$HOME/.claude.json" 2>/dev/null)
+  _GBRAIN_MCP_ENTRY=$(jq -c --arg cwd "$PWD" '.mcpServers.gbrain // ((.projects // {}) | to_entries | map(select((.key as $k | $cwd == $k or ($cwd | startswith($k + "/"))) and ((try .value.mcpServers.gbrain catch null) != null))) | sort_by(.key | length) | last | .value.mcpServers.gbrain) // empty' "$HOME/.claude.json" 2>/dev/null)
+  _GBRAIN_MCP_TYPE=$(printf '%s' "$_GBRAIN_MCP_ENTRY" | jq -r '.type // .transport // empty' 2>/dev/null)
   case "$_GBRAIN_MCP_TYPE" in
     url|http|sse) _GBRAIN_MCP_MODE="remote-http" ;;
     stdio) _GBRAIN_MCP_MODE="local-stdio" ;;
@@ -546,7 +549,7 @@ fi
 if [ "$_GBRAIN_MCP_MODE" = "remote-http" ]; then
   # Remote-MCP mode: local artifacts sync is a no-op (brain admin's server
   # pulls from GitHub/GitLab). Show the user this is by design, not broken.
-  _GBRAIN_HOST=$(jq -r '.mcpServers.gbrain.url // empty' "$HOME/.claude.json" 2>/dev/null | sed -E 's|^https?://([^/:]+).*|\1|' | head -1 | tr -cd 'A-Za-z0-9._-')
+  _GBRAIN_HOST=$(printf '%s' "${_GBRAIN_MCP_ENTRY:-}" | jq -r '.url // empty' 2>/dev/null | sed -E 's|^https?://([^/:]+).*|\1|' | head -1 | tr -cd 'A-Za-z0-9._-')
   echo "ARTIFACTS_SYNC: remote-mode (managed by brain server ${_GBRAIN_HOST:-remote})"
 elif [ -d "$_GSTACK_HOME/.git" ] && [ "$_BRAIN_SYNC_MODE" != "off" ]; then
   _BRAIN_QUEUE_DEPTH=0
diff --git a/health/SKILL.md b/health/SKILL.md
index 352cd3e04..2466a83c5 100644
--- a/health/SKILL.md
+++ b/health/SKILL.md
@@ -506,10 +506,13 @@ _BRAIN_SYNC_MODE=$("$_BRAIN_CONFIG_BIN" get artifacts_sync_mode 2>/dev/null || e
 # Detect remote-MCP mode (Path 4 of /setup-gbrain). Local artifacts sync is
 # a no-op in remote mode; the brain server pulls from GitHub/GitLab on its
 # own cadence. Read claude.json directly to keep this preamble fast (no
-# subprocess to claude CLI on every skill start).
+# subprocess to claude CLI on every skill start). Both registration scopes
+# are read (#2499): user scope, then the nearest-ancestor project scope.
 _GBRAIN_MCP_MODE="none"
+_GBRAIN_MCP_ENTRY=""
 if command -v jq >/dev/null 2>&1 && [ -f "$HOME/.claude.json" ]; then
-  _GBRAIN_MCP_TYPE=$(jq -r '.mcpServers.gbrain.type // .mcpServers.gbrain.transport // empty' "$HOME/.claude.json" 2>/dev/null)
+  _GBRAIN_MCP_ENTRY=$(jq -c --arg cwd "$PWD" '.mcpServers.gbrain // ((.projects // {}) | to_entries | map(select((.key as $k | $cwd == $k or ($cwd | startswith($k + "/"))) and ((try .value.mcpServers.gbrain catch null) != null))) | sort_by(.key | length) | last | .value.mcpServers.gbrain) // empty' "$HOME/.claude.json" 2>/dev/null)
+  _GBRAIN_MCP_TYPE=$(printf '%s' "$_GBRAIN_MCP_ENTRY" | jq -r '.type // .transport // empty' 2>/dev/null)
   case "$_GBRAIN_MCP_TYPE" in
     url|http|sse) _GBRAIN_MCP_MODE="remote-http" ;;
     stdio) _GBRAIN_MCP_MODE="local-stdio" ;;
@@ -544,7 +547,7 @@ fi
 if [ "$_GBRAIN_MCP_MODE" = "remote-http" ]; then
   # Remote-MCP mode: local artifacts sync is a no-op (brain admin's server
   # pulls from GitHub/GitLab). Show the user this is by design, not broken.
-  _GBRAIN_HOST=$(jq -r '.mcpServers.gbrain.url // empty' "$HOME/.claude.json" 2>/dev/null | sed -E 's|^https?://([^/:]+).*|\1|' | head -1 | tr -cd 'A-Za-z0-9._-')
+  _GBRAIN_HOST=$(printf '%s' "${_GBRAIN_MCP_ENTRY:-}" | jq -r '.url // empty' 2>/dev/null | sed -E 's|^https?://([^/:]+).*|\1|' | head -1 | tr -cd 'A-Za-z0-9._-')
   echo "ARTIFACTS_SYNC: remote-mode (managed by brain server ${_GBRAIN_HOST:-remote})"
 elif [ -d "$_GSTACK_HOME/.git" ] && [ "$_BRAIN_SYNC_MODE" != "off" ]; then
   _BRAIN_QUEUE_DEPTH=0
diff --git a/investigate/SKILL.md b/investigate/SKILL.md
index ebdc934a2..81b872d0c 100644
--- a/investigate/SKILL.md
+++ b/investigate/SKILL.md
@@ -545,10 +545,13 @@ _BRAIN_SYNC_MODE=$("$_BRAIN_CONFIG_BIN" get artifacts_sync_mode 2>/dev/null || e
 # Detect remote-MCP mode (Path 4 of /setup-gbrain). Local artifacts sync is
 # a no-op in remote mode; the brain server pulls from GitHub/GitLab on its
 # own cadence. Read claude.json directly to keep this preamble fast (no
-# subprocess to claude CLI on every skill start).
+# subprocess to claude CLI on every skill start). Both registration scopes
+# are read (#2499): user scope, then the nearest-ancestor project scope.
 _GBRAIN_MCP_MODE="none"
+_GBRAIN_MCP_ENTRY=""
 if command -v jq >/dev/null 2>&1 && [ -f "$HOME/.claude.json" ]; then
-  _GBRAIN_MCP_TYPE=$(jq -r '.mcpServers.gbrain.type // .mcpServers.gbrain.transport // empty' "$HOME/.claude.json" 2>/dev/null)
+  _GBRAIN_MCP_ENTRY=$(jq -c --arg cwd "$PWD" '.mcpServers.gbrain // ((.projects // {}) | to_entries | map(select((.key as $k | $cwd == $k or ($cwd | startswith($k + "/"))) and ((try .value.mcpServers.gbrain catch null) != null))) | sort_by(.key | length) | last | .value.mcpServers.gbrain) // empty' "$HOME/.claude.json" 2>/dev/null)
+  _GBRAIN_MCP_TYPE=$(printf '%s' "$_GBRAIN_MCP_ENTRY" | jq -r '.type // .transport // empty' 2>/dev/null)
   case "$_GBRAIN_MCP_TYPE" in
     url|http|sse) _GBRAIN_MCP_MODE="remote-http" ;;
     stdio) _GBRAIN_MCP_MODE="local-stdio" ;;
@@ -583,7 +586,7 @@ fi
 if [ "$_GBRAIN_MCP_MODE" = "remote-http" ]; then
   # Remote-MCP mode: local artifacts sync is a no-op (brain admin's server
   # pulls from GitHub/GitLab). Show the user this is by design, not broken.
-  _GBRAIN_HOST=$(jq -r '.mcpServers.gbrain.url // empty' "$HOME/.claude.json" 2>/dev/null | sed -E 's|^https?://([^/:]+).*|\1|' | head -1 | tr -cd 'A-Za-z0-9._-')
+  _GBRAIN_HOST=$(printf '%s' "${_GBRAIN_MCP_ENTRY:-}" | jq -r '.url // empty' 2>/dev/null | sed -E 's|^https?://([^/:]+).*|\1|' | head -1 | tr -cd 'A-Za-z0-9._-')
   echo "ARTIFACTS_SYNC: remote-mode (managed by brain server ${_GBRAIN_HOST:-remote})"
 elif [ -d "$_GSTACK_HOME/.git" ] && [ "$_BRAIN_SYNC_MODE" != "off" ]; then
   _BRAIN_QUEUE_DEPTH=0
diff --git a/ios-clean/SKILL.md b/ios-clean/SKILL.md
index c0a36bfd6..f5f3fdf81 100644
--- a/ios-clean/SKILL.md
+++ b/ios-clean/SKILL.md
@@ -508,10 +508,13 @@ _BRAIN_SYNC_MODE=$("$_BRAIN_CONFIG_BIN" get artifacts_sync_mode 2>/dev/null || e
 # Detect remote-MCP mode (Path 4 of /setup-gbrain). Local artifacts sync is
 # a no-op in remote mode; the brain server pulls from GitHub/GitLab on its
 # own cadence. Read claude.json directly to keep this preamble fast (no
-# subprocess to claude CLI on every skill start).
+# subprocess to claude CLI on every skill start). Both registration scopes
+# are read (#2499): user scope, then the nearest-ancestor project scope.
 _GBRAIN_MCP_MODE="none"
+_GBRAIN_MCP_ENTRY=""
 if command -v jq >/dev/null 2>&1 && [ -f "$HOME/.claude.json" ]; then
-  _GBRAIN_MCP_TYPE=$(jq -r '.mcpServers.gbrain.type // .mcpServers.gbrain.transport // empty' "$HOME/.claude.json" 2>/dev/null)
+  _GBRAIN_MCP_ENTRY=$(jq -c --arg cwd "$PWD" '.mcpServers.gbrain // ((.projects // {}) | to_entries | map(select((.key as $k | $cwd == $k or ($cwd | startswith($k + "/"))) and ((try .value.mcpServers.gbrain catch null) != null))) | sort_by(.key | length) | last | .value.mcpServers.gbrain) // empty' "$HOME/.claude.json" 2>/dev/null)
+  _GBRAIN_MCP_TYPE=$(printf '%s' "$_GBRAIN_MCP_ENTRY" | jq -r '.type // .transport // empty' 2>/dev/null)
   case "$_GBRAIN_MCP_TYPE" in
     url|http|sse) _GBRAIN_MCP_MODE="remote-http" ;;
     stdio) _GBRAIN_MCP_MODE="local-stdio" ;;
@@ -546,7 +549,7 @@ fi
 if [ "$_GBRAIN_MCP_MODE" = "remote-http" ]; then
   # Remote-MCP mode: local artifacts sync is a no-op (brain admin's server
   # pulls from GitHub/GitLab). Show the user this is by design, not broken.
-  _GBRAIN_HOST=$(jq -r '.mcpServers.gbrain.url // empty' "$HOME/.claude.json" 2>/dev/null | sed -E 's|^https?://([^/:]+).*|\1|' | head -1 | tr -cd 'A-Za-z0-9._-')
+  _GBRAIN_HOST=$(printf '%s' "${_GBRAIN_MCP_ENTRY:-}" | jq -r '.url // empty' 2>/dev/null | sed -E 's|^https?://([^/:]+).*|\1|' | head -1 | tr -cd 'A-Za-z0-9._-')
   echo "ARTIFACTS_SYNC: remote-mode (managed by brain server ${_GBRAIN_HOST:-remote})"
 elif [ -d "$_GSTACK_HOME/.git" ] && [ "$_BRAIN_SYNC_MODE" != "off" ]; then
   _BRAIN_QUEUE_DEPTH=0
diff --git a/ios-design-review/SKILL.md b/ios-design-review/SKILL.md
index f61cf9710..185a24c98 100644
--- a/ios-design-review/SKILL.md
+++ b/ios-design-review/SKILL.md
@@ -510,10 +510,13 @@ _BRAIN_SYNC_MODE=$("$_BRAIN_CONFIG_BIN" get artifacts_sync_mode 2>/dev/null || e
 # Detect remote-MCP mode (Path 4 of /setup-gbrain). Local artifacts sync is
 # a no-op in remote mode; the brain server pulls from GitHub/GitLab on its
 # own cadence. Read claude.json directly to keep this preamble fast (no
-# subprocess to claude CLI on every skill start).
+# subprocess to claude CLI on every skill start). Both registration scopes
+# are read (#2499): user scope, then the nearest-ancestor project scope.
 _GBRAIN_MCP_MODE="none"
+_GBRAIN_MCP_ENTRY=""
 if command -v jq >/dev/null 2>&1 && [ -f "$HOME/.claude.json" ]; then
-  _GBRAIN_MCP_TYPE=$(jq -r '.mcpServers.gbrain.type // .mcpServers.gbrain.transport // empty' "$HOME/.claude.json" 2>/dev/null)
+  _GBRAIN_MCP_ENTRY=$(jq -c --arg cwd "$PWD" '.mcpServers.gbrain // ((.projects // {}) | to_entries | map(select((.key as $k | $cwd == $k or ($cwd | startswith($k + "/"))) and ((try .value.mcpServers.gbrain catch null) != null))) | sort_by(.key | length) | last | .value.mcpServers.gbrain) // empty' "$HOME/.claude.json" 2>/dev/null)
+  _GBRAIN_MCP_TYPE=$(printf '%s' "$_GBRAIN_MCP_ENTRY" | jq -r '.type // .transport // empty' 2>/dev/null)
   case "$_GBRAIN_MCP_TYPE" in
     url|http|sse) _GBRAIN_MCP_MODE="remote-http" ;;
     stdio) _GBRAIN_MCP_MODE="local-stdio" ;;
@@ -548,7 +551,7 @@ fi
 if [ "$_GBRAIN_MCP_MODE" = "remote-http" ]; then
   # Remote-MCP mode: local artifacts sync is a no-op (brain admin's server
   # pulls from GitHub/GitLab). Show the user this is by design, not broken.
-  _GBRAIN_HOST=$(jq -r '.mcpServers.gbrain.url // empty' "$HOME/.claude.json" 2>/dev/null | sed -E 's|^https?://([^/:]+).*|\1|' | head -1 | tr -cd 'A-Za-z0-9._-')
+  _GBRAIN_HOST=$(printf '%s' "${_GBRAIN_MCP_ENTRY:-}" | jq -r '.url // empty' 2>/dev/null | sed -E 's|^https?://([^/:]+).*|\1|' | head -1 | tr -cd 'A-Za-z0-9._-')
   echo "ARTIFACTS_SYNC: remote-mode (managed by brain server ${_GBRAIN_HOST:-remote})"
 elif [ -d "$_GSTACK_HOME/.git" ] && [ "$_BRAIN_SYNC_MODE" != "off" ]; then
   _BRAIN_QUEUE_DEPTH=0
diff --git a/ios-fix/SKILL.md b/ios-fix/SKILL.md
index ec12406c2..989b0a6ac 100644
--- a/ios-fix/SKILL.md
+++ b/ios-fix/SKILL.md
@@ -511,10 +511,13 @@ _BRAIN_SYNC_MODE=$("$_BRAIN_CONFIG_BIN" get artifacts_sync_mode 2>/dev/null || e
 # Detect remote-MCP mode (Path 4 of /setup-gbrain). Local artifacts sync is
 # a no-op in remote mode; the brain server pulls from GitHub/GitLab on its
 # own cadence. Read claude.json directly to keep this preamble fast (no
-# subprocess to claude CLI on every skill start).
+# subprocess to claude CLI on every skill start). Both registration scopes
+# are read (#2499): user scope, then the nearest-ancestor project scope.
 _GBRAIN_MCP_MODE="none"
+_GBRAIN_MCP_ENTRY=""
 if command -v jq >/dev/null 2>&1 && [ -f "$HOME/.claude.json" ]; then
-  _GBRAIN_MCP_TYPE=$(jq -r '.mcpServers.gbrain.type // .mcpServers.gbrain.transport // empty' "$HOME/.claude.json" 2>/dev/null)
+  _GBRAIN_MCP_ENTRY=$(jq -c --arg cwd "$PWD" '.mcpServers.gbrain // ((.projects // {}) | to_entries | map(select((.key as $k | $cwd == $k or ($cwd | startswith($k + "/"))) and ((try .value.mcpServers.gbrain catch null) != null))) | sort_by(.key | length) | last | .value.mcpServers.gbrain) // empty' "$HOME/.claude.json" 2>/dev/null)
+  _GBRAIN_MCP_TYPE=$(printf '%s' "$_GBRAIN_MCP_ENTRY" | jq -r '.type // .transport // empty' 2>/dev/null)
   case "$_GBRAIN_MCP_TYPE" in
     url|http|sse) _GBRAIN_MCP_MODE="remote-http" ;;
     stdio) _GBRAIN_MCP_MODE="local-stdio" ;;
@@ -549,7 +552,7 @@ fi
 if [ "$_GBRAIN_MCP_MODE" = "remote-http" ]; then
   # Remote-MCP mode: local artifacts sync is a no-op (brain admin's server
   # pulls from GitHub/GitLab). Show the user this is by design, not broken.
-  _GBRAIN_HOST=$(jq -r '.mcpServers.gbrain.url // empty' "$HOME/.claude.json" 2>/dev/null | sed -E 's|^https?://([^/:]+).*|\1|' | head -1 | tr -cd 'A-Za-z0-9._-')
+  _GBRAIN_HOST=$(printf '%s' "${_GBRAIN_MCP_ENTRY:-}" | jq -r '.url // empty' 2>/dev/null | sed -E 's|^https?://([^/:]+).*|\1|' | head -1 | tr -cd 'A-Za-z0-9._-')
   echo "ARTIFACTS_SYNC: remote-mode (managed by brain server ${_GBRAIN_HOST:-remote})"
 elif [ -d "$_GSTACK_HOME/.git" ] && [ "$_BRAIN_SYNC_MODE" != "off" ]; then
   _BRAIN_QUEUE_DEPTH=0
diff --git a/ios-qa/SKILL.md b/ios-qa/SKILL.md
index 6e56ea4ed..72b02a7f6 100644
--- a/ios-qa/SKILL.md
+++ b/ios-qa/SKILL.md
@@ -514,10 +514,13 @@ _BRAIN_SYNC_MODE=$("$_BRAIN_CONFIG_BIN" get artifacts_sync_mode 2>/dev/null || e
 # Detect remote-MCP mode (Path 4 of /setup-gbrain). Local artifacts sync is
 # a no-op in remote mode; the brain server pulls from GitHub/GitLab on its
 # own cadence. Read claude.json directly to keep this preamble fast (no
-# subprocess to claude CLI on every skill start).
+# subprocess to claude CLI on every skill start). Both registration scopes
+# are read (#2499): user scope, then the nearest-ancestor project scope.
 _GBRAIN_MCP_MODE="none"
+_GBRAIN_MCP_ENTRY=""
 if command -v jq >/dev/null 2>&1 && [ -f "$HOME/.claude.json" ]; then
-  _GBRAIN_MCP_TYPE=$(jq -r '.mcpServers.gbrain.type // .mcpServers.gbrain.transport // empty' "$HOME/.claude.json" 2>/dev/null)
+  _GBRAIN_MCP_ENTRY=$(jq -c --arg cwd "$PWD" '.mcpServers.gbrain // ((.projects // {}) | to_entries | map(select((.key as $k | $cwd == $k or ($cwd | startswith($k + "/"))) and ((try .value.mcpServers.gbrain catch null) != null))) | sort_by(.key | length) | last | .value.mcpServers.gbrain) // empty' "$HOME/.claude.json" 2>/dev/null)
+  _GBRAIN_MCP_TYPE=$(printf '%s' "$_GBRAIN_MCP_ENTRY" | jq -r '.type // .transport // empty' 2>/dev/null)
   case "$_GBRAIN_MCP_TYPE" in
     url|http|sse) _GBRAIN_MCP_MODE="remote-http" ;;
     stdio) _GBRAIN_MCP_MODE="local-stdio" ;;
@@ -552,7 +555,7 @@ fi
 if [ "$_GBRAIN_MCP_MODE" = "remote-http" ]; then
   # Remote-MCP mode: local artifacts sync is a no-op (brain admin's server
   # pulls from GitHub/GitLab). Show the user this is by design, not broken.
-  _GBRAIN_HOST=$(jq -r '.mcpServers.gbrain.url // empty' "$HOME/.claude.json" 2>/dev/null | sed -E 's|^https?://([^/:]+).*|\1|' | head -1 | tr -cd 'A-Za-z0-9._-')
+  _GBRAIN_HOST=$(printf '%s' "${_GBRAIN_MCP_ENTRY:-}" | jq -r '.url // empty' 2>/dev/null | sed -E 's|^https?://([^/:]+).*|\1|' | head -1 | tr -cd 'A-Za-z0-9._-')
   echo "ARTIFACTS_SYNC: remote-mode (managed by brain server ${_GBRAIN_HOST:-remote})"
 elif [ -d "$_GSTACK_HOME/.git" ] && [ "$_BRAIN_SYNC_MODE" != "off" ]; then
   _BRAIN_QUEUE_DEPTH=0
diff --git a/ios-sync/SKILL.md b/ios-sync/SKILL.md
index 18c709d09..4fdc28866 100644
--- a/ios-sync/SKILL.md
+++ b/ios-sync/SKILL.md
@@ -508,10 +508,13 @@ _BRAIN_SYNC_MODE=$("$_BRAIN_CONFIG_BIN" get artifacts_sync_mode 2>/dev/null || e
 # Detect remote-MCP mode (Path 4 of /setup-gbrain). Local artifacts sync is
 # a no-op in remote mode; the brain server pulls from GitHub/GitLab on its
 # own cadence. Read claude.json directly to keep this preamble fast (no
-# subprocess to claude CLI on every skill start).
+# subprocess to claude CLI on every skill start). Both registration scopes
+# are read (#2499): user scope, then the nearest-ancestor project scope.
 _GBRAIN_MCP_MODE="none"
+_GBRAIN_MCP_ENTRY=""
 if command -v jq >/dev/null 2>&1 && [ -f "$HOME/.claude.json" ]; then
-  _GBRAIN_MCP_TYPE=$(jq -r '.mcpServers.gbrain.type // .mcpServers.gbrain.transport // empty' "$HOME/.claude.json" 2>/dev/null)
+  _GBRAIN_MCP_ENTRY=$(jq -c --arg cwd "$PWD" '.mcpServers.gbrain // ((.projects // {}) | to_entries | map(select((.key as $k | $cwd == $k or ($cwd | startswith($k + "/"))) and ((try .value.mcpServers.gbrain catch null) != null))) | sort_by(.key | length) | last | .value.mcpServers.gbrain) // empty' "$HOME/.claude.json" 2>/dev/null)
+  _GBRAIN_MCP_TYPE=$(printf '%s' "$_GBRAIN_MCP_ENTRY" | jq -r '.type // .transport // empty' 2>/dev/null)
   case "$_GBRAIN_MCP_TYPE" in
     url|http|sse) _GBRAIN_MCP_MODE="remote-http" ;;
     stdio) _GBRAIN_MCP_MODE="local-stdio" ;;
@@ -546,7 +549,7 @@ fi
 if [ "$_GBRAIN_MCP_MODE" = "remote-http" ]; then
   # Remote-MCP mode: local artifacts sync is a no-op (brain admin's server
   # pulls from GitHub/GitLab). Show the user this is by design, not broken.
-  _GBRAIN_HOST=$(jq -r '.mcpServers.gbrain.url // empty' "$HOME/.claude.json" 2>/dev/null | sed -E 's|^https?://([^/:]+).*|\1|' | head -1 | tr -cd 'A-Za-z0-9._-')
+  _GBRAIN_HOST=$(printf '%s' "${_GBRAIN_MCP_ENTRY:-}" | jq -r '.url // empty' 2>/dev/null | sed -E 's|^https?://([^/:]+).*|\1|' | head -1 | tr -cd 'A-Za-z0-9._-')
   echo "ARTIFACTS_SYNC: remote-mode (managed by brain server ${_GBRAIN_HOST:-remote})"
 elif [ -d "$_GSTACK_HOME/.git" ] && [ "$_BRAIN_SYNC_MODE" != "off" ]; then
   _BRAIN_QUEUE_DEPTH=0
diff --git a/land-and-deploy/SKILL.md b/land-and-deploy/SKILL.md
index 51bf460f3..67813624a 100644
--- a/land-and-deploy/SKILL.md
+++ b/land-and-deploy/SKILL.md
@@ -503,10 +503,13 @@ _BRAIN_SYNC_MODE=$("$_BRAIN_CONFIG_BIN" get artifacts_sync_mode 2>/dev/null || e
 # Detect remote-MCP mode (Path 4 of /setup-gbrain). Local artifacts sync is
 # a no-op in remote mode; the brain server pulls from GitHub/GitLab on its
 # own cadence. Read claude.json directly to keep this preamble fast (no
-# subprocess to claude CLI on every skill start).
+# subprocess to claude CLI on every skill start). Both registration scopes
+# are read (#2499): user scope, then the nearest-ancestor project scope.
 _GBRAIN_MCP_MODE="none"
+_GBRAIN_MCP_ENTRY=""
 if command -v jq >/dev/null 2>&1 && [ -f "$HOME/.claude.json" ]; then
-  _GBRAIN_MCP_TYPE=$(jq -r '.mcpServers.gbrain.type // .mcpServers.gbrain.transport // empty' "$HOME/.claude.json" 2>/dev/null)
+  _GBRAIN_MCP_ENTRY=$(jq -c --arg cwd "$PWD" '.mcpServers.gbrain // ((.projects // {}) | to_entries | map(select((.key as $k | $cwd == $k or ($cwd | startswith($k + "/"))) and ((try .value.mcpServers.gbrain catch null) != null))) | sort_by(.key | length) | last | .value.mcpServers.gbrain) // empty' "$HOME/.claude.json" 2>/dev/null)
+  _GBRAIN_MCP_TYPE=$(printf '%s' "$_GBRAIN_MCP_ENTRY" | jq -r '.type // .transport // empty' 2>/dev/null)
   case "$_GBRAIN_MCP_TYPE" in
     url|http|sse) _GBRAIN_MCP_MODE="remote-http" ;;
     stdio) _GBRAIN_MCP_MODE="local-stdio" ;;
@@ -541,7 +544,7 @@ fi
 if [ "$_GBRAIN_MCP_MODE" = "remote-http" ]; then
   # Remote-MCP mode: local artifacts sync is a no-op (brain admin's server
   # pulls from GitHub/GitLab). Show the user this is by design, not broken.
-  _GBRAIN_HOST=$(jq -r '.mcpServers.gbrain.url // empty' "$HOME/.claude.json" 2>/dev/null | sed -E 's|^https?://([^/:]+).*|\1|' | head -1 | tr -cd 'A-Za-z0-9._-')
+  _GBRAIN_HOST=$(printf '%s' "${_GBRAIN_MCP_ENTRY:-}" | jq -r '.url // empty' 2>/dev/null | sed -E 's|^https?://([^/:]+).*|\1|' | head -1 | tr -cd 'A-Za-z0-9._-')
   echo "ARTIFACTS_SYNC: remote-mode (managed by brain server ${_GBRAIN_HOST:-remote})"
 elif [ -d "$_GSTACK_HOME/.git" ] && [ "$_BRAIN_SYNC_MODE" != "off" ]; then
   _BRAIN_QUEUE_DEPTH=0
diff --git a/landing-report/SKILL.md b/landing-report/SKILL.md
index 49b15e993..114e54210 100644
--- a/landing-report/SKILL.md
+++ b/landing-report/SKILL.md
@@ -505,10 +505,13 @@ _BRAIN_SYNC_MODE=$("$_BRAIN_CONFIG_BIN" get artifacts_sync_mode 2>/dev/null || e
 # Detect remote-MCP mode (Path 4 of /setup-gbrain). Local artifacts sync is
 # a no-op in remote mode; the brain server pulls from GitHub/GitLab on its
 # own cadence. Read claude.json directly to keep this preamble fast (no
-# subprocess to claude CLI on every skill start).
+# subprocess to claude CLI on every skill start). Both registration scopes
+# are read (#2499): user scope, then the nearest-ancestor project scope.
 _GBRAIN_MCP_MODE="none"
+_GBRAIN_MCP_ENTRY=""
 if command -v jq >/dev/null 2>&1 && [ -f "$HOME/.claude.json" ]; then
-  _GBRAIN_MCP_TYPE=$(jq -r '.mcpServers.gbrain.type // .mcpServers.gbrain.transport // empty' "$HOME/.claude.json" 2>/dev/null)
+  _GBRAIN_MCP_ENTRY=$(jq -c --arg cwd "$PWD" '.mcpServers.gbrain // ((.projects // {}) | to_entries | map(select((.key as $k | $cwd == $k or ($cwd | startswith($k + "/"))) and ((try .value.mcpServers.gbrain catch null) != null))) | sort_by(.key | length) | last | .value.mcpServers.gbrain) // empty' "$HOME/.claude.json" 2>/dev/null)
+  _GBRAIN_MCP_TYPE=$(printf '%s' "$_GBRAIN_MCP_ENTRY" | jq -r '.type // .transport // empty' 2>/dev/null)
   case "$_GBRAIN_MCP_TYPE" in
     url|http|sse) _GBRAIN_MCP_MODE="remote-http" ;;
     stdio) _GBRAIN_MCP_MODE="local-stdio" ;;
@@ -543,7 +546,7 @@ fi
 if [ "$_GBRAIN_MCP_MODE" = "remote-http" ]; then
   # Remote-MCP mode: local artifacts sync is a no-op (brain admin's server
   # pulls from GitHub/GitLab). Show the user this is by design, not broken.
-  _GBRAIN_HOST=$(jq -r '.mcpServers.gbrain.url // empty' "$HOME/.claude.json" 2>/dev/null | sed -E 's|^https?://([^/:]+).*|\1|' | head -1 | tr -cd 'A-Za-z0-9._-')
+  _GBRAIN_HOST=$(printf '%s' "${_GBRAIN_MCP_ENTRY:-}" | jq -r '.url // empty' 2>/dev/null | sed -E 's|^https?://([^/:]+).*|\1|' | head -1 | tr -cd 'A-Za-z0-9._-')
   echo "ARTIFACTS_SYNC: remote-mode (managed by brain server ${_GBRAIN_HOST:-remote})"
 elif [ -d "$_GSTACK_HOME/.git" ] && [ "$_BRAIN_SYNC_MODE" != "off" ]; then
   _BRAIN_QUEUE_DEPTH=0
diff --git a/learn/SKILL.md b/learn/SKILL.md
index d3b82b52f..eccf8a3fd 100644
--- a/learn/SKILL.md
+++ b/learn/SKILL.md
@@ -506,10 +506,13 @@ _BRAIN_SYNC_MODE=$("$_BRAIN_CONFIG_BIN" get artifacts_sync_mode 2>/dev/null || e
 # Detect remote-MCP mode (Path 4 of /setup-gbrain). Local artifacts sync is
 # a no-op in remote mode; the brain server pulls from GitHub/GitLab on its
 # own cadence. Read claude.json directly to keep this preamble fast (no
-# subprocess to claude CLI on every skill start).
+# subprocess to claude CLI on every skill start). Both registration scopes
+# are read (#2499): user scope, then the nearest-ancestor project scope.
 _GBRAIN_MCP_MODE="none"
+_GBRAIN_MCP_ENTRY=""
 if command -v jq >/dev/null 2>&1 && [ -f "$HOME/.claude.json" ]; then
-  _GBRAIN_MCP_TYPE=$(jq -r '.mcpServers.gbrain.type // .mcpServers.gbrain.transport // empty' "$HOME/.claude.json" 2>/dev/null)
+  _GBRAIN_MCP_ENTRY=$(jq -c --arg cwd "$PWD" '.mcpServers.gbrain // ((.projects // {}) | to_entries | map(select((.key as $k | $cwd == $k or ($cwd | startswith($k + "/"))) and ((try .value.mcpServers.gbrain catch null) != null))) | sort_by(.key | length) | last | .value.mcpServers.gbrain) // empty' "$HOME/.claude.json" 2>/dev/null)
+  _GBRAIN_MCP_TYPE=$(printf '%s' "$_GBRAIN_MCP_ENTRY" | jq -r '.type // .transport // empty' 2>/dev/null)
   case "$_GBRAIN_MCP_TYPE" in
     url|http|sse) _GBRAIN_MCP_MODE="remote-http" ;;
     stdio) _GBRAIN_MCP_MODE="local-stdio" ;;
@@ -544,7 +547,7 @@ fi
 if [ "$_GBRAIN_MCP_MODE" = "remote-http" ]; then
   # Remote-MCP mode: local artifacts sync is a no-op (brain admin's server
   # pulls from GitHub/GitLab). Show the user this is by design, not broken.
-  _GBRAIN_HOST=$(jq -r '.mcpServers.gbrain.url // empty' "$HOME/.claude.json" 2>/dev/null | sed -E 's|^https?://([^/:]+).*|\1|' | head -1 | tr -cd 'A-Za-z0-9._-')
+  _GBRAIN_HOST=$(printf '%s' "${_GBRAIN_MCP_ENTRY:-}" | jq -r '.url // empty' 2>/dev/null | sed -E 's|^https?://([^/:]+).*|\1|' | head -1 | tr -cd 'A-Za-z0-9._-')
   echo "ARTIFACTS_SYNC: remote-mode (managed by brain server ${_GBRAIN_HOST:-remote})"
 elif [ -d "$_GSTACK_HOME/.git" ] && [ "$_BRAIN_SYNC_MODE" != "off" ]; then
   _BRAIN_QUEUE_DEPTH=0
diff --git a/make-pdf/SKILL.md b/make-pdf/SKILL.md
index 666bad78c..8ddfe5c51 100644
--- a/make-pdf/SKILL.md
+++ b/make-pdf/SKILL.md
@@ -416,10 +416,13 @@ _BRAIN_SYNC_MODE=$("$_BRAIN_CONFIG_BIN" get artifacts_sync_mode 2>/dev/null || e
 # Detect remote-MCP mode (Path 4 of /setup-gbrain). Local artifacts sync is
 # a no-op in remote mode; the brain server pulls from GitHub/GitLab on its
 # own cadence. Read claude.json directly to keep this preamble fast (no
-# subprocess to claude CLI on every skill start).
+# subprocess to claude CLI on every skill start). Both registration scopes
+# are read (#2499): user scope, then the nearest-ancestor project scope.
 _GBRAIN_MCP_MODE="none"
+_GBRAIN_MCP_ENTRY=""
 if command -v jq >/dev/null 2>&1 && [ -f "$HOME/.claude.json" ]; then
-  _GBRAIN_MCP_TYPE=$(jq -r '.mcpServers.gbrain.type // .mcpServers.gbrain.transport // empty' "$HOME/.claude.json" 2>/dev/null)
+  _GBRAIN_MCP_ENTRY=$(jq -c --arg cwd "$PWD" '.mcpServers.gbrain // ((.projects // {}) | to_entries | map(select((.key as $k | $cwd == $k or ($cwd | startswith($k + "/"))) and ((try .value.mcpServers.gbrain catch null) != null))) | sort_by(.key | length) | last | .value.mcpServers.gbrain) // empty' "$HOME/.claude.json" 2>/dev/null)
+  _GBRAIN_MCP_TYPE=$(printf '%s' "$_GBRAIN_MCP_ENTRY" | jq -r '.type // .transport // empty' 2>/dev/null)
   case "$_GBRAIN_MCP_TYPE" in
     url|http|sse) _GBRAIN_MCP_MODE="remote-http" ;;
     stdio) _GBRAIN_MCP_MODE="local-stdio" ;;
@@ -454,7 +457,7 @@ fi
 if [ "$_GBRAIN_MCP_MODE" = "remote-http" ]; then
   # Remote-MCP mode: local artifacts sync is a no-op (brain admin's server
   # pulls from GitHub/GitLab). Show the user this is by design, not broken.
-  _GBRAIN_HOST=$(jq -r '.mcpServers.gbrain.url // empty' "$HOME/.claude.json" 2>/dev/null | sed -E 's|^https?://([^/:]+).*|\1|' | head -1 | tr -cd 'A-Za-z0-9._-')
+  _GBRAIN_HOST=$(printf '%s' "${_GBRAIN_MCP_ENTRY:-}" | jq -r '.url // empty' 2>/dev/null | sed -E 's|^https?://([^/:]+).*|\1|' | head -1 | tr -cd 'A-Za-z0-9._-')
   echo "ARTIFACTS_SYNC: remote-mode (managed by brain server ${_GBRAIN_HOST:-remote})"
 elif [ -d "$_GSTACK_HOME/.git" ] && [ "$_BRAIN_SYNC_MODE" != "off" ]; then
   _BRAIN_QUEUE_DEPTH=0
diff --git a/office-hours/SKILL.md b/office-hours/SKILL.md
index c4b7254c0..2b4eff1f2 100644
--- a/office-hours/SKILL.md
+++ b/office-hours/SKILL.md
@@ -541,10 +541,13 @@ _BRAIN_SYNC_MODE=$("$_BRAIN_CONFIG_BIN" get artifacts_sync_mode 2>/dev/null || e
 # Detect remote-MCP mode (Path 4 of /setup-gbrain). Local artifacts sync is
 # a no-op in remote mode; the brain server pulls from GitHub/GitLab on its
 # own cadence. Read claude.json directly to keep this preamble fast (no
-# subprocess to claude CLI on every skill start).
+# subprocess to claude CLI on every skill start). Both registration scopes
+# are read (#2499): user scope, then the nearest-ancestor project scope.
 _GBRAIN_MCP_MODE="none"
+_GBRAIN_MCP_ENTRY=""
 if command -v jq >/dev/null 2>&1 && [ -f "$HOME/.claude.json" ]; then
-  _GBRAIN_MCP_TYPE=$(jq -r '.mcpServers.gbrain.type // .mcpServers.gbrain.transport // empty' "$HOME/.claude.json" 2>/dev/null)
+  _GBRAIN_MCP_ENTRY=$(jq -c --arg cwd "$PWD" '.mcpServers.gbrain // ((.projects // {}) | to_entries | map(select((.key as $k | $cwd == $k or ($cwd | startswith($k + "/"))) and ((try .value.mcpServers.gbrain catch null) != null))) | sort_by(.key | length) | last | .value.mcpServers.gbrain) // empty' "$HOME/.claude.json" 2>/dev/null)
+  _GBRAIN_MCP_TYPE=$(printf '%s' "$_GBRAIN_MCP_ENTRY" | jq -r '.type // .transport // empty' 2>/dev/null)
   case "$_GBRAIN_MCP_TYPE" in
     url|http|sse) _GBRAIN_MCP_MODE="remote-http" ;;
     stdio) _GBRAIN_MCP_MODE="local-stdio" ;;
@@ -579,7 +582,7 @@ fi
 if [ "$_GBRAIN_MCP_MODE" = "remote-http" ]; then
   # Remote-MCP mode: local artifacts sync is a no-op (brain admin's server
   # pulls from GitHub/GitLab). Show the user this is by design, not broken.
-  _GBRAIN_HOST=$(jq -r '.mcpServers.gbrain.url // empty' "$HOME/.claude.json" 2>/dev/null | sed -E 's|^https?://([^/:]+).*|\1|' | head -1 | tr -cd 'A-Za-z0-9._-')
+  _GBRAIN_HOST=$(printf '%s' "${_GBRAIN_MCP_ENTRY:-}" | jq -r '.url // empty' 2>/dev/null | sed -E 's|^https?://([^/:]+).*|\1|' | head -1 | tr -cd 'A-Za-z0-9._-')
   echo "ARTIFACTS_SYNC: remote-mode (managed by brain server ${_GBRAIN_HOST:-remote})"
 elif [ -d "$_GSTACK_HOME/.git" ] && [ "$_BRAIN_SYNC_MODE" != "off" ]; then
   _BRAIN_QUEUE_DEPTH=0
diff --git a/open-gstack-browser/SKILL.md b/open-gstack-browser/SKILL.md
index 559eaa3b6..a1b98c3ca 100644
--- a/open-gstack-browser/SKILL.md
+++ b/open-gstack-browser/SKILL.md
@@ -379,10 +379,13 @@ _BRAIN_SYNC_MODE=$("$_BRAIN_CONFIG_BIN" get artifacts_sync_mode 2>/dev/null || e
 # Detect remote-MCP mode (Path 4 of /setup-gbrain). Local artifacts sync is
 # a no-op in remote mode; the brain server pulls from GitHub/GitLab on its
 # own cadence. Read claude.json directly to keep this preamble fast (no
-# subprocess to claude CLI on every skill start).
+# subprocess to claude CLI on every skill start). Both registration scopes
+# are read (#2499): user scope, then the nearest-ancestor project scope.
 _GBRAIN_MCP_MODE="none"
+_GBRAIN_MCP_ENTRY=""
 if command -v jq >/dev/null 2>&1 && [ -f "$HOME/.claude.json" ]; then
-  _GBRAIN_MCP_TYPE=$(jq -r '.mcpServers.gbrain.type // .mcpServers.gbrain.transport // empty' "$HOME/.claude.json" 2>/dev/null)
+  _GBRAIN_MCP_ENTRY=$(jq -c --arg cwd "$PWD" '.mcpServers.gbrain // ((.projects // {}) | to_entries | map(select((.key as $k | $cwd == $k or ($cwd | startswith($k + "/"))) and ((try .value.mcpServers.gbrain catch null) != null))) | sort_by(.key | length) | last | .value.mcpServers.gbrain) // empty' "$HOME/.claude.json" 2>/dev/null)
+  _GBRAIN_MCP_TYPE=$(printf '%s' "$_GBRAIN_MCP_ENTRY" | jq -r '.type // .transport // empty' 2>/dev/null)
   case "$_GBRAIN_MCP_TYPE" in
     url|http|sse) _GBRAIN_MCP_MODE="remote-http" ;;
     stdio) _GBRAIN_MCP_MODE="local-stdio" ;;
@@ -417,7 +420,7 @@ fi
 if [ "$_GBRAIN_MCP_MODE" = "remote-http" ]; then
   # Remote-MCP mode: local artifacts sync is a no-op (brain admin's server
   # pulls from GitHub/GitLab). Show the user this is by design, not broken.
-  _GBRAIN_HOST=$(jq -r '.mcpServers.gbrain.url // empty' "$HOME/.claude.json" 2>/dev/null | sed -E 's|^https?://([^/:]+).*|\1|' | head -1 | tr -cd 'A-Za-z0-9._-')
+  _GBRAIN_HOST=$(printf '%s' "${_GBRAIN_MCP_ENTRY:-}" | jq -r '.url // empty' 2>/dev/null | sed -E 's|^https?://([^/:]+).*|\1|' | head -1 | tr -cd 'A-Za-z0-9._-')
   echo "ARTIFACTS_SYNC: remote-mode (managed by brain server ${_GBRAIN_HOST:-remote})"
 elif [ -d "$_GSTACK_HOME/.git" ] && [ "$_BRAIN_SYNC_MODE" != "off" ]; then
   _BRAIN_QUEUE_DEPTH=0
diff --git a/pair-agent/SKILL.md b/pair-agent/SKILL.md
index af608c243..2aa276d2d 100644
--- a/pair-agent/SKILL.md
+++ b/pair-agent/SKILL.md
@@ -506,10 +506,13 @@ _BRAIN_SYNC_MODE=$("$_BRAIN_CONFIG_BIN" get artifacts_sync_mode 2>/dev/null || e
 # Detect remote-MCP mode (Path 4 of /setup-gbrain). Local artifacts sync is
 # a no-op in remote mode; the brain server pulls from GitHub/GitLab on its
 # own cadence. Read claude.json directly to keep this preamble fast (no
-# subprocess to claude CLI on every skill start).
+# subprocess to claude CLI on every skill start). Both registration scopes
+# are read (#2499): user scope, then the nearest-ancestor project scope.
 _GBRAIN_MCP_MODE="none"
+_GBRAIN_MCP_ENTRY=""
 if command -v jq >/dev/null 2>&1 && [ -f "$HOME/.claude.json" ]; then
-  _GBRAIN_MCP_TYPE=$(jq -r '.mcpServers.gbrain.type // .mcpServers.gbrain.transport // empty' "$HOME/.claude.json" 2>/dev/null)
+  _GBRAIN_MCP_ENTRY=$(jq -c --arg cwd "$PWD" '.mcpServers.gbrain // ((.projects // {}) | to_entries | map(select((.key as $k | $cwd == $k or ($cwd | startswith($k + "/"))) and ((try .value.mcpServers.gbrain catch null) != null))) | sort_by(.key | length) | last | .value.mcpServers.gbrain) // empty' "$HOME/.claude.json" 2>/dev/null)
+  _GBRAIN_MCP_TYPE=$(printf '%s' "$_GBRAIN_MCP_ENTRY" | jq -r '.type // .transport // empty' 2>/dev/null)
   case "$_GBRAIN_MCP_TYPE" in
     url|http|sse) _GBRAIN_MCP_MODE="remote-http" ;;
     stdio) _GBRAIN_MCP_MODE="local-stdio" ;;
@@ -544,7 +547,7 @@ fi
 if [ "$_GBRAIN_MCP_MODE" = "remote-http" ]; then
   # Remote-MCP mode: local artifacts sync is a no-op (brain admin's server
   # pulls from GitHub/GitLab). Show the user this is by design, not broken.
-  _GBRAIN_HOST=$(jq -r '.mcpServers.gbrain.url // empty' "$HOME/.claude.json" 2>/dev/null | sed -E 's|^https?://([^/:]+).*|\1|' | head -1 | tr -cd 'A-Za-z0-9._-')
+  _GBRAIN_HOST=$(printf '%s' "${_GBRAIN_MCP_ENTRY:-}" | jq -r '.url // empty' 2>/dev/null | sed -E 's|^https?://([^/:]+).*|\1|' | head -1 | tr -cd 'A-Za-z0-9._-')
   echo "ARTIFACTS_SYNC: remote-mode (managed by brain server ${_GBRAIN_HOST:-remote})"
 elif [ -d "$_GSTACK_HOME/.git" ] && [ "$_BRAIN_SYNC_MODE" != "off" ]; then
   _BRAIN_QUEUE_DEPTH=0
diff --git a/plan-ceo-review/SKILL.md b/plan-ceo-review/SKILL.md
index 3d5e9b911..3c7607e0f 100644
--- a/plan-ceo-review/SKILL.md
+++ b/plan-ceo-review/SKILL.md
@@ -535,10 +535,13 @@ _BRAIN_SYNC_MODE=$("$_BRAIN_CONFIG_BIN" get artifacts_sync_mode 2>/dev/null || e
 # Detect remote-MCP mode (Path 4 of /setup-gbrain). Local artifacts sync is
 # a no-op in remote mode; the brain server pulls from GitHub/GitLab on its
 # own cadence. Read claude.json directly to keep this preamble fast (no
-# subprocess to claude CLI on every skill start).
+# subprocess to claude CLI on every skill start). Both registration scopes
+# are read (#2499): user scope, then the nearest-ancestor project scope.
 _GBRAIN_MCP_MODE="none"
+_GBRAIN_MCP_ENTRY=""
 if command -v jq >/dev/null 2>&1 && [ -f "$HOME/.claude.json" ]; then
-  _GBRAIN_MCP_TYPE=$(jq -r '.mcpServers.gbrain.type // .mcpServers.gbrain.transport // empty' "$HOME/.claude.json" 2>/dev/null)
+  _GBRAIN_MCP_ENTRY=$(jq -c --arg cwd "$PWD" '.mcpServers.gbrain // ((.projects // {}) | to_entries | map(select((.key as $k | $cwd == $k or ($cwd | startswith($k + "/"))) and ((try .value.mcpServers.gbrain catch null) != null))) | sort_by(.key | length) | last | .value.mcpServers.gbrain) // empty' "$HOME/.claude.json" 2>/dev/null)
+  _GBRAIN_MCP_TYPE=$(printf '%s' "$_GBRAIN_MCP_ENTRY" | jq -r '.type // .transport // empty' 2>/dev/null)
   case "$_GBRAIN_MCP_TYPE" in
     url|http|sse) _GBRAIN_MCP_MODE="remote-http" ;;
     stdio) _GBRAIN_MCP_MODE="local-stdio" ;;
@@ -573,7 +576,7 @@ fi
 if [ "$_GBRAIN_MCP_MODE" = "remote-http" ]; then
   # Remote-MCP mode: local artifacts sync is a no-op (brain admin's server
   # pulls from GitHub/GitLab). Show the user this is by design, not broken.
-  _GBRAIN_HOST=$(jq -r '.mcpServers.gbrain.url // empty' "$HOME/.claude.json" 2>/dev/null | sed -E 's|^https?://([^/:]+).*|\1|' | head -1 | tr -cd 'A-Za-z0-9._-')
+  _GBRAIN_HOST=$(printf '%s' "${_GBRAIN_MCP_ENTRY:-}" | jq -r '.url // empty' 2>/dev/null | sed -E 's|^https?://([^/:]+).*|\1|' | head -1 | tr -cd 'A-Za-z0-9._-')
   echo "ARTIFACTS_SYNC: remote-mode (managed by brain server ${_GBRAIN_HOST:-remote})"
 elif [ -d "$_GSTACK_HOME/.git" ] && [ "$_BRAIN_SYNC_MODE" != "off" ]; then
   _BRAIN_QUEUE_DEPTH=0
diff --git a/plan-design-review/SKILL.md b/plan-design-review/SKILL.md
index 525e5df68..d7fb3a74a 100644
--- a/plan-design-review/SKILL.md
+++ b/plan-design-review/SKILL.md
@@ -507,10 +507,13 @@ _BRAIN_SYNC_MODE=$("$_BRAIN_CONFIG_BIN" get artifacts_sync_mode 2>/dev/null || e
 # Detect remote-MCP mode (Path 4 of /setup-gbrain). Local artifacts sync is
 # a no-op in remote mode; the brain server pulls from GitHub/GitLab on its
 # own cadence. Read claude.json directly to keep this preamble fast (no
-# subprocess to claude CLI on every skill start).
+# subprocess to claude CLI on every skill start). Both registration scopes
+# are read (#2499): user scope, then the nearest-ancestor project scope.
 _GBRAIN_MCP_MODE="none"
+_GBRAIN_MCP_ENTRY=""
 if command -v jq >/dev/null 2>&1 && [ -f "$HOME/.claude.json" ]; then
-  _GBRAIN_MCP_TYPE=$(jq -r '.mcpServers.gbrain.type // .mcpServers.gbrain.transport // empty' "$HOME/.claude.json" 2>/dev/null)
+  _GBRAIN_MCP_ENTRY=$(jq -c --arg cwd "$PWD" '.mcpServers.gbrain // ((.projects // {}) | to_entries | map(select((.key as $k | $cwd == $k or ($cwd | startswith($k + "/"))) and ((try .value.mcpServers.gbrain catch null) != null))) | sort_by(.key | length) | last | .value.mcpServers.gbrain) // empty' "$HOME/.claude.json" 2>/dev/null)
+  _GBRAIN_MCP_TYPE=$(printf '%s' "$_GBRAIN_MCP_ENTRY" | jq -r '.type // .transport // empty' 2>/dev/null)
   case "$_GBRAIN_MCP_TYPE" in
     url|http|sse) _GBRAIN_MCP_MODE="remote-http" ;;
     stdio) _GBRAIN_MCP_MODE="local-stdio" ;;
@@ -545,7 +548,7 @@ fi
 if [ "$_GBRAIN_MCP_MODE" = "remote-http" ]; then
   # Remote-MCP mode: local artifacts sync is a no-op (brain admin's server
   # pulls from GitHub/GitLab). Show the user this is by design, not broken.
-  _GBRAIN_HOST=$(jq -r '.mcpServers.gbrain.url // empty' "$HOME/.claude.json" 2>/dev/null | sed -E 's|^https?://([^/:]+).*|\1|' | head -1 | tr -cd 'A-Za-z0-9._-')
+  _GBRAIN_HOST=$(printf '%s' "${_GBRAIN_MCP_ENTRY:-}" | jq -r '.url // empty' 2>/dev/null | sed -E 's|^https?://([^/:]+).*|\1|' | head -1 | tr -cd 'A-Za-z0-9._-')
   echo "ARTIFACTS_SYNC: remote-mode (managed by brain server ${_GBRAIN_HOST:-remote})"
 elif [ -d "$_GSTACK_HOME/.git" ] && [ "$_BRAIN_SYNC_MODE" != "off" ]; then
   _BRAIN_QUEUE_DEPTH=0
diff --git a/plan-devex-review/SKILL.md b/plan-devex-review/SKILL.md
index 447cd3a1f..d80bfba77 100644
--- a/plan-devex-review/SKILL.md
+++ b/plan-devex-review/SKILL.md
@@ -513,10 +513,13 @@ _BRAIN_SYNC_MODE=$("$_BRAIN_CONFIG_BIN" get artifacts_sync_mode 2>/dev/null || e
 # Detect remote-MCP mode (Path 4 of /setup-gbrain). Local artifacts sync is
 # a no-op in remote mode; the brain server pulls from GitHub/GitLab on its
 # own cadence. Read claude.json directly to keep this preamble fast (no
-# subprocess to claude CLI on every skill start).
+# subprocess to claude CLI on every skill start). Both registration scopes
+# are read (#2499): user scope, then the nearest-ancestor project scope.
 _GBRAIN_MCP_MODE="none"
+_GBRAIN_MCP_ENTRY=""
 if command -v jq >/dev/null 2>&1 && [ -f "$HOME/.claude.json" ]; then
-  _GBRAIN_MCP_TYPE=$(jq -r '.mcpServers.gbrain.type // .mcpServers.gbrain.transport // empty' "$HOME/.claude.json" 2>/dev/null)
+  _GBRAIN_MCP_ENTRY=$(jq -c --arg cwd "$PWD" '.mcpServers.gbrain // ((.projects // {}) | to_entries | map(select((.key as $k | $cwd == $k or ($cwd | startswith($k + "/"))) and ((try .value.mcpServers.gbrain catch null) != null))) | sort_by(.key | length) | last | .value.mcpServers.gbrain) // empty' "$HOME/.claude.json" 2>/dev/null)
+  _GBRAIN_MCP_TYPE=$(printf '%s' "$_GBRAIN_MCP_ENTRY" | jq -r '.type // .transport // empty' 2>/dev/null)
   case "$_GBRAIN_MCP_TYPE" in
     url|http|sse) _GBRAIN_MCP_MODE="remote-http" ;;
     stdio) _GBRAIN_MCP_MODE="local-stdio" ;;
@@ -551,7 +554,7 @@ fi
 if [ "$_GBRAIN_MCP_MODE" = "remote-http" ]; then
   # Remote-MCP mode: local artifacts sync is a no-op (brain admin's server
   # pulls from GitHub/GitLab). Show the user this is by design, not broken.
-  _GBRAIN_HOST=$(jq -r '.mcpServers.gbrain.url // empty' "$HOME/.claude.json" 2>/dev/null | sed -E 's|^https?://([^/:]+).*|\1|' | head -1 | tr -cd 'A-Za-z0-9._-')
+  _GBRAIN_HOST=$(printf '%s' "${_GBRAIN_MCP_ENTRY:-}" | jq -r '.url // empty' 2>/dev/null | sed -E 's|^https?://([^/:]+).*|\1|' | head -1 | tr -cd 'A-Za-z0-9._-')
   echo "ARTIFACTS_SYNC: remote-mode (managed by brain server ${_GBRAIN_HOST:-remote})"
 elif [ -d "$_GSTACK_HOME/.git" ] && [ "$_BRAIN_SYNC_MODE" != "off" ]; then
   _BRAIN_QUEUE_DEPTH=0
diff --git a/plan-eng-review/SKILL.md b/plan-eng-review/SKILL.md
index 22afb1c10..d196dba7f 100644
--- a/plan-eng-review/SKILL.md
+++ b/plan-eng-review/SKILL.md
@@ -511,10 +511,13 @@ _BRAIN_SYNC_MODE=$("$_BRAIN_CONFIG_BIN" get artifacts_sync_mode 2>/dev/null || e
 # Detect remote-MCP mode (Path 4 of /setup-gbrain). Local artifacts sync is
 # a no-op in remote mode; the brain server pulls from GitHub/GitLab on its
 # own cadence. Read claude.json directly to keep this preamble fast (no
-# subprocess to claude CLI on every skill start).
+# subprocess to claude CLI on every skill start). Both registration scopes
+# are read (#2499): user scope, then the nearest-ancestor project scope.
 _GBRAIN_MCP_MODE="none"
+_GBRAIN_MCP_ENTRY=""
 if command -v jq >/dev/null 2>&1 && [ -f "$HOME/.claude.json" ]; then
-  _GBRAIN_MCP_TYPE=$(jq -r '.mcpServers.gbrain.type // .mcpServers.gbrain.transport // empty' "$HOME/.claude.json" 2>/dev/null)
+  _GBRAIN_MCP_ENTRY=$(jq -c --arg cwd "$PWD" '.mcpServers.gbrain // ((.projects // {}) | to_entries | map(select((.key as $k | $cwd == $k or ($cwd | startswith($k + "/"))) and ((try .value.mcpServers.gbrain catch null) != null))) | sort_by(.key | length) | last | .value.mcpServers.gbrain) // empty' "$HOME/.claude.json" 2>/dev/null)
+  _GBRAIN_MCP_TYPE=$(printf '%s' "$_GBRAIN_MCP_ENTRY" | jq -r '.type // .transport // empty' 2>/dev/null)
   case "$_GBRAIN_MCP_TYPE" in
     url|http|sse) _GBRAIN_MCP_MODE="remote-http" ;;
     stdio) _GBRAIN_MCP_MODE="local-stdio" ;;
@@ -549,7 +552,7 @@ fi
 if [ "$_GBRAIN_MCP_MODE" = "remote-http" ]; then
   # Remote-MCP mode: local artifacts sync is a no-op (brain admin's server
   # pulls from GitHub/GitLab). Show the user this is by design, not broken.
-  _GBRAIN_HOST=$(jq -r '.mcpServers.gbrain.url // empty' "$HOME/.claude.json" 2>/dev/null | sed -E 's|^https?://([^/:]+).*|\1|' | head -1 | tr -cd 'A-Za-z0-9._-')
+  _GBRAIN_HOST=$(printf '%s' "${_GBRAIN_MCP_ENTRY:-}" | jq -r '.url // empty' 2>/dev/null | sed -E 's|^https?://([^/:]+).*|\1|' | head -1 | tr -cd 'A-Za-z0-9._-')
   echo "ARTIFACTS_SYNC: remote-mode (managed by brain server ${_GBRAIN_HOST:-remote})"
 elif [ -d "$_GSTACK_HOME/.git" ] && [ "$_BRAIN_SYNC_MODE" != "off" ]; then
   _BRAIN_QUEUE_DEPTH=0
diff --git a/plan-tune/SKILL.md b/plan-tune/SKILL.md
index de473b9a2..2f1e265fb 100644
--- a/plan-tune/SKILL.md
+++ b/plan-tune/SKILL.md
@@ -516,10 +516,13 @@ _BRAIN_SYNC_MODE=$("$_BRAIN_CONFIG_BIN" get artifacts_sync_mode 2>/dev/null || e
 # Detect remote-MCP mode (Path 4 of /setup-gbrain). Local artifacts sync is
 # a no-op in remote mode; the brain server pulls from GitHub/GitLab on its
 # own cadence. Read claude.json directly to keep this preamble fast (no
-# subprocess to claude CLI on every skill start).
+# subprocess to claude CLI on every skill start). Both registration scopes
+# are read (#2499): user scope, then the nearest-ancestor project scope.
 _GBRAIN_MCP_MODE="none"
+_GBRAIN_MCP_ENTRY=""
 if command -v jq >/dev/null 2>&1 && [ -f "$HOME/.claude.json" ]; then
-  _GBRAIN_MCP_TYPE=$(jq -r '.mcpServers.gbrain.type // .mcpServers.gbrain.transport // empty' "$HOME/.claude.json" 2>/dev/null)
+  _GBRAIN_MCP_ENTRY=$(jq -c --arg cwd "$PWD" '.mcpServers.gbrain // ((.projects // {}) | to_entries | map(select((.key as $k | $cwd == $k or ($cwd | startswith($k + "/"))) and ((try .value.mcpServers.gbrain catch null) != null))) | sort_by(.key | length) | last | .value.mcpServers.gbrain) // empty' "$HOME/.claude.json" 2>/dev/null)
+  _GBRAIN_MCP_TYPE=$(printf '%s' "$_GBRAIN_MCP_ENTRY" | jq -r '.type // .transport // empty' 2>/dev/null)
   case "$_GBRAIN_MCP_TYPE" in
     url|http|sse) _GBRAIN_MCP_MODE="remote-http" ;;
     stdio) _GBRAIN_MCP_MODE="local-stdio" ;;
@@ -554,7 +557,7 @@ fi
 if [ "$_GBRAIN_MCP_MODE" = "remote-http" ]; then
   # Remote-MCP mode: local artifacts sync is a no-op (brain admin's server
   # pulls from GitHub/GitLab). Show the user this is by design, not broken.
-  _GBRAIN_HOST=$(jq -r '.mcpServers.gbrain.url // empty' "$HOME/.claude.json" 2>/dev/null | sed -E 's|^https?://([^/:]+).*|\1|' | head -1 | tr -cd 'A-Za-z0-9._-')
+  _GBRAIN_HOST=$(printf '%s' "${_GBRAIN_MCP_ENTRY:-}" | jq -r '.url // empty' 2>/dev/null | sed -E 's|^https?://([^/:]+).*|\1|' | head -1 | tr -cd 'A-Za-z0-9._-')
   echo "ARTIFACTS_SYNC: remote-mode (managed by brain server ${_GBRAIN_HOST:-remote})"
 elif [ -d "$_GSTACK_HOME/.git" ] && [ "$_BRAIN_SYNC_MODE" != "off" ]; then
   _BRAIN_QUEUE_DEPTH=0
diff --git a/qa-only/SKILL.md b/qa-only/SKILL.md
index eafa358de..3209628b7 100644
--- a/qa-only/SKILL.md
+++ b/qa-only/SKILL.md
@@ -506,10 +506,13 @@ _BRAIN_SYNC_MODE=$("$_BRAIN_CONFIG_BIN" get artifacts_sync_mode 2>/dev/null || e
 # Detect remote-MCP mode (Path 4 of /setup-gbrain). Local artifacts sync is
 # a no-op in remote mode; the brain server pulls from GitHub/GitLab on its
 # own cadence. Read claude.json directly to keep this preamble fast (no
-# subprocess to claude CLI on every skill start).
+# subprocess to claude CLI on every skill start). Both registration scopes
+# are read (#2499): user scope, then the nearest-ancestor project scope.
 _GBRAIN_MCP_MODE="none"
+_GBRAIN_MCP_ENTRY=""
 if command -v jq >/dev/null 2>&1 && [ -f "$HOME/.claude.json" ]; then
-  _GBRAIN_MCP_TYPE=$(jq -r '.mcpServers.gbrain.type // .mcpServers.gbrain.transport // empty' "$HOME/.claude.json" 2>/dev/null)
+  _GBRAIN_MCP_ENTRY=$(jq -c --arg cwd "$PWD" '.mcpServers.gbrain // ((.projects // {}) | to_entries | map(select((.key as $k | $cwd == $k or ($cwd | startswith($k + "/"))) and ((try .value.mcpServers.gbrain catch null) != null))) | sort_by(.key | length) | last | .value.mcpServers.gbrain) // empty' "$HOME/.claude.json" 2>/dev/null)
+  _GBRAIN_MCP_TYPE=$(printf '%s' "$_GBRAIN_MCP_ENTRY" | jq -r '.type // .transport // empty' 2>/dev/null)
   case "$_GBRAIN_MCP_TYPE" in
     url|http|sse) _GBRAIN_MCP_MODE="remote-http" ;;
     stdio) _GBRAIN_MCP_MODE="local-stdio" ;;
@@ -544,7 +547,7 @@ fi
 if [ "$_GBRAIN_MCP_MODE" = "remote-http" ]; then
   # Remote-MCP mode: local artifacts sync is a no-op (brain admin's server
   # pulls from GitHub/GitLab). Show the user this is by design, not broken.
-  _GBRAIN_HOST=$(jq -r '.mcpServers.gbrain.url // empty' "$HOME/.claude.json" 2>/dev/null | sed -E 's|^https?://([^/:]+).*|\1|' | head -1 | tr -cd 'A-Za-z0-9._-')
+  _GBRAIN_HOST=$(printf '%s' "${_GBRAIN_MCP_ENTRY:-}" | jq -r '.url // empty' 2>/dev/null | sed -E 's|^https?://([^/:]+).*|\1|' | head -1 | tr -cd 'A-Za-z0-9._-')
   echo "ARTIFACTS_SYNC: remote-mode (managed by brain server ${_GBRAIN_HOST:-remote})"
 elif [ -d "$_GSTACK_HOME/.git" ] && [ "$_BRAIN_SYNC_MODE" != "off" ]; then
   _BRAIN_QUEUE_DEPTH=0
diff --git a/qa/SKILL.md b/qa/SKILL.md
index b11981476..4fb7f86c2 100644
--- a/qa/SKILL.md
+++ b/qa/SKILL.md
@@ -512,10 +512,13 @@ _BRAIN_SYNC_MODE=$("$_BRAIN_CONFIG_BIN" get artifacts_sync_mode 2>/dev/null || e
 # Detect remote-MCP mode (Path 4 of /setup-gbrain). Local artifacts sync is
 # a no-op in remote mode; the brain server pulls from GitHub/GitLab on its
 # own cadence. Read claude.json directly to keep this preamble fast (no
-# subprocess to claude CLI on every skill start).
+# subprocess to claude CLI on every skill start). Both registration scopes
+# are read (#2499): user scope, then the nearest-ancestor project scope.
 _GBRAIN_MCP_MODE="none"
+_GBRAIN_MCP_ENTRY=""
 if command -v jq >/dev/null 2>&1 && [ -f "$HOME/.claude.json" ]; then
-  _GBRAIN_MCP_TYPE=$(jq -r '.mcpServers.gbrain.type // .mcpServers.gbrain.transport // empty' "$HOME/.claude.json" 2>/dev/null)
+  _GBRAIN_MCP_ENTRY=$(jq -c --arg cwd "$PWD" '.mcpServers.gbrain // ((.projects // {}) | to_entries | map(select((.key as $k | $cwd == $k or ($cwd | startswith($k + "/"))) and ((try .value.mcpServers.gbrain catch null) != null))) | sort_by(.key | length) | last | .value.mcpServers.gbrain) // empty' "$HOME/.claude.json" 2>/dev/null)
+  _GBRAIN_MCP_TYPE=$(printf '%s' "$_GBRAIN_MCP_ENTRY" | jq -r '.type // .transport // empty' 2>/dev/null)
   case "$_GBRAIN_MCP_TYPE" in
     url|http|sse) _GBRAIN_MCP_MODE="remote-http" ;;
     stdio) _GBRAIN_MCP_MODE="local-stdio" ;;
@@ -550,7 +553,7 @@ fi
 if [ "$_GBRAIN_MCP_MODE" = "remote-http" ]; then
   # Remote-MCP mode: local artifacts sync is a no-op (brain admin's server
   # pulls from GitHub/GitLab). Show the user this is by design, not broken.
-  _GBRAIN_HOST=$(jq -r '.mcpServers.gbrain.url // empty' "$HOME/.claude.json" 2>/dev/null | sed -E 's|^https?://([^/:]+).*|\1|' | head -1 | tr -cd 'A-Za-z0-9._-')
+  _GBRAIN_HOST=$(printf '%s' "${_GBRAIN_MCP_ENTRY:-}" | jq -r '.url // empty' 2>/dev/null | sed -E 's|^https?://([^/:]+).*|\1|' | head -1 | tr -cd 'A-Za-z0-9._-')
   echo "ARTIFACTS_SYNC: remote-mode (managed by brain server ${_GBRAIN_HOST:-remote})"
 elif [ -d "$_GSTACK_HOME/.git" ] && [ "$_BRAIN_SYNC_MODE" != "off" ]; then
   _BRAIN_QUEUE_DEPTH=0
diff --git a/retro/SKILL.md b/retro/SKILL.md
index f6fd85d12..ef723d679 100644
--- a/retro/SKILL.md
+++ b/retro/SKILL.md
@@ -526,10 +526,13 @@ _BRAIN_SYNC_MODE=$("$_BRAIN_CONFIG_BIN" get artifacts_sync_mode 2>/dev/null || e
 # Detect remote-MCP mode (Path 4 of /setup-gbrain). Local artifacts sync is
 # a no-op in remote mode; the brain server pulls from GitHub/GitLab on its
 # own cadence. Read claude.json directly to keep this preamble fast (no
-# subprocess to claude CLI on every skill start).
+# subprocess to claude CLI on every skill start). Both registration scopes
+# are read (#2499): user scope, then the nearest-ancestor project scope.
 _GBRAIN_MCP_MODE="none"
+_GBRAIN_MCP_ENTRY=""
 if command -v jq >/dev/null 2>&1 && [ -f "$HOME/.claude.json" ]; then
-  _GBRAIN_MCP_TYPE=$(jq -r '.mcpServers.gbrain.type // .mcpServers.gbrain.transport // empty' "$HOME/.claude.json" 2>/dev/null)
+  _GBRAIN_MCP_ENTRY=$(jq -c --arg cwd "$PWD" '.mcpServers.gbrain // ((.projects // {}) | to_entries | map(select((.key as $k | $cwd == $k or ($cwd | startswith($k + "/"))) and ((try .value.mcpServers.gbrain catch null) != null))) | sort_by(.key | length) | last | .value.mcpServers.gbrain) // empty' "$HOME/.claude.json" 2>/dev/null)
+  _GBRAIN_MCP_TYPE=$(printf '%s' "$_GBRAIN_MCP_ENTRY" | jq -r '.type // .transport // empty' 2>/dev/null)
   case "$_GBRAIN_MCP_TYPE" in
     url|http|sse) _GBRAIN_MCP_MODE="remote-http" ;;
     stdio) _GBRAIN_MCP_MODE="local-stdio" ;;
@@ -564,7 +567,7 @@ fi
 if [ "$_GBRAIN_MCP_MODE" = "remote-http" ]; then
   # Remote-MCP mode: local artifacts sync is a no-op (brain admin's server
   # pulls from GitHub/GitLab). Show the user this is by design, not broken.
-  _GBRAIN_HOST=$(jq -r '.mcpServers.gbrain.url // empty' "$HOME/.claude.json" 2>/dev/null | sed -E 's|^https?://([^/:]+).*|\1|' | head -1 | tr -cd 'A-Za-z0-9._-')
+  _GBRAIN_HOST=$(printf '%s' "${_GBRAIN_MCP_ENTRY:-}" | jq -r '.url // empty' 2>/dev/null | sed -E 's|^https?://([^/:]+).*|\1|' | head -1 | tr -cd 'A-Za-z0-9._-')
   echo "ARTIFACTS_SYNC: remote-mode (managed by brain server ${_GBRAIN_HOST:-remote})"
 elif [ -d "$_GSTACK_HOME/.git" ] && [ "$_BRAIN_SYNC_MODE" != "off" ]; then
   _BRAIN_QUEUE_DEPTH=0
diff --git a/review/SKILL.md b/review/SKILL.md
index 263973daf..6099d2b91 100644
--- a/review/SKILL.md
+++ b/review/SKILL.md
@@ -508,10 +508,13 @@ _BRAIN_SYNC_MODE=$("$_BRAIN_CONFIG_BIN" get artifacts_sync_mode 2>/dev/null || e
 # Detect remote-MCP mode (Path 4 of /setup-gbrain). Local artifacts sync is
 # a no-op in remote mode; the brain server pulls from GitHub/GitLab on its
 # own cadence. Read claude.json directly to keep this preamble fast (no
-# subprocess to claude CLI on every skill start).
+# subprocess to claude CLI on every skill start). Both registration scopes
+# are read (#2499): user scope, then the nearest-ancestor project scope.
 _GBRAIN_MCP_MODE="none"
+_GBRAIN_MCP_ENTRY=""
 if command -v jq >/dev/null 2>&1 && [ -f "$HOME/.claude.json" ]; then
-  _GBRAIN_MCP_TYPE=$(jq -r '.mcpServers.gbrain.type // .mcpServers.gbrain.transport // empty' "$HOME/.claude.json" 2>/dev/null)
+  _GBRAIN_MCP_ENTRY=$(jq -c --arg cwd "$PWD" '.mcpServers.gbrain // ((.projects // {}) | to_entries | map(select((.key as $k | $cwd == $k or ($cwd | startswith($k + "/"))) and ((try .value.mcpServers.gbrain catch null) != null))) | sort_by(.key | length) | last | .value.mcpServers.gbrain) // empty' "$HOME/.claude.json" 2>/dev/null)
+  _GBRAIN_MCP_TYPE=$(printf '%s' "$_GBRAIN_MCP_ENTRY" | jq -r '.type // .transport // empty' 2>/dev/null)
   case "$_GBRAIN_MCP_TYPE" in
     url|http|sse) _GBRAIN_MCP_MODE="remote-http" ;;
     stdio) _GBRAIN_MCP_MODE="local-stdio" ;;
@@ -546,7 +549,7 @@ fi
 if [ "$_GBRAIN_MCP_MODE" = "remote-http" ]; then
   # Remote-MCP mode: local artifacts sync is a no-op (brain admin's server
   # pulls from GitHub/GitLab). Show the user this is by design, not broken.
-  _GBRAIN_HOST=$(jq -r '.mcpServers.gbrain.url // empty' "$HOME/.claude.json" 2>/dev/null | sed -E 's|^https?://([^/:]+).*|\1|' | head -1 | tr -cd 'A-Za-z0-9._-')
+  _GBRAIN_HOST=$(printf '%s' "${_GBRAIN_MCP_ENTRY:-}" | jq -r '.url // empty' 2>/dev/null | sed -E 's|^https?://([^/:]+).*|\1|' | head -1 | tr -cd 'A-Za-z0-9._-')
   echo "ARTIFACTS_SYNC: remote-mode (managed by brain server ${_GBRAIN_HOST:-remote})"
 elif [ -d "$_GSTACK_HOME/.git" ] && [ "$_BRAIN_SYNC_MODE" != "off" ]; then
   _BRAIN_QUEUE_DEPTH=0
diff --git a/scrape/SKILL.md b/scrape/SKILL.md
index f3ba51a60..87d174fbf 100644
--- a/scrape/SKILL.md
+++ b/scrape/SKILL.md
@@ -380,10 +380,13 @@ _BRAIN_SYNC_MODE=$("$_BRAIN_CONFIG_BIN" get artifacts_sync_mode 2>/dev/null || e
 # Detect remote-MCP mode (Path 4 of /setup-gbrain). Local artifacts sync is
 # a no-op in remote mode; the brain server pulls from GitHub/GitLab on its
 # own cadence. Read claude.json directly to keep this preamble fast (no
-# subprocess to claude CLI on every skill start).
+# subprocess to claude CLI on every skill start). Both registration scopes
+# are read (#2499): user scope, then the nearest-ancestor project scope.
 _GBRAIN_MCP_MODE="none"
+_GBRAIN_MCP_ENTRY=""
 if command -v jq >/dev/null 2>&1 && [ -f "$HOME/.claude.json" ]; then
-  _GBRAIN_MCP_TYPE=$(jq -r '.mcpServers.gbrain.type // .mcpServers.gbrain.transport // empty' "$HOME/.claude.json" 2>/dev/null)
+  _GBRAIN_MCP_ENTRY=$(jq -c --arg cwd "$PWD" '.mcpServers.gbrain // ((.projects // {}) | to_entries | map(select((.key as $k | $cwd == $k or ($cwd | startswith($k + "/"))) and ((try .value.mcpServers.gbrain catch null) != null))) | sort_by(.key | length) | last | .value.mcpServers.gbrain) // empty' "$HOME/.claude.json" 2>/dev/null)
+  _GBRAIN_MCP_TYPE=$(printf '%s' "$_GBRAIN_MCP_ENTRY" | jq -r '.type // .transport // empty' 2>/dev/null)
   case "$_GBRAIN_MCP_TYPE" in
     url|http|sse) _GBRAIN_MCP_MODE="remote-http" ;;
     stdio) _GBRAIN_MCP_MODE="local-stdio" ;;
@@ -418,7 +421,7 @@ fi
 if [ "$_GBRAIN_MCP_MODE" = "remote-http" ]; then
   # Remote-MCP mode: local artifacts sync is a no-op (brain admin's server
   # pulls from GitHub/GitLab). Show the user this is by design, not broken.
-  _GBRAIN_HOST=$(jq -r '.mcpServers.gbrain.url // empty' "$HOME/.claude.json" 2>/dev/null | sed -E 's|^https?://([^/:]+).*|\1|' | head -1 | tr -cd 'A-Za-z0-9._-')
+  _GBRAIN_HOST=$(printf '%s' "${_GBRAIN_MCP_ENTRY:-}" | jq -r '.url // empty' 2>/dev/null | sed -E 's|^https?://([^/:]+).*|\1|' | head -1 | tr -cd 'A-Za-z0-9._-')
   echo "ARTIFACTS_SYNC: remote-mode (managed by brain server ${_GBRAIN_HOST:-remote})"
 elif [ -d "$_GSTACK_HOME/.git" ] && [ "$_BRAIN_SYNC_MODE" != "off" ]; then
   _BRAIN_QUEUE_DEPTH=0
diff --git a/scripts/resolvers/preamble/generate-brain-sync-block.ts b/scripts/resolvers/preamble/generate-brain-sync-block.ts
index 0b0a022a1..ae1ab5778 100644
--- a/scripts/resolvers/preamble/generate-brain-sync-block.ts
+++ b/scripts/resolvers/preamble/generate-brain-sync-block.ts
@@ -30,6 +30,27 @@
 import type { TemplateContext } from '../types';
 import { quoteSafePath } from '../types';
 
+/**
+ * Shared jq sub-expression resolving the gbrain MCP registration entry
+ * (#2499). Claude Code registers MCP servers at TWO scopes in
+ * ~/.claude.json: user scope (.mcpServers.gbrain) and project scope
+ * (.projects["/abs/path"].mcpServers.gbrain — what `claude mcp add`
+ * WITHOUT --scope user writes). Reading only user scope makes a correctly
+ * configured project-scoped brain invisible: brain-aware blocks suppress,
+ * remote-mode sync is never recognised, nothing errors.
+ *
+ * Resolution order: user scope first, then the nearest-ancestor project
+ * entry for $PWD that actually carries a gbrain server (longest matching
+ * key with a path-boundary check, so nested repos pick their own
+ * registration, /a/repo never matches /a/repo2, and a nested project
+ * WITHOUT gbrain doesn't shadow its parent's registration). The emitted
+ * bash resolves the entry ONCE into _GBRAIN_MCP_ENTRY (compact JSON) and
+ * extracts fields from that variable — one jq parse of claude.json per
+ * skill start, and the long expression appears once per rendered SKILL.md.
+ */
+const GBRAIN_MCP_ENTRY_JQ =
+  '.mcpServers.gbrain // ((.projects // {}) | to_entries | map(select((.key as $k | $cwd == $k or ($cwd | startswith($k + "/"))) and ((try .value.mcpServers.gbrain catch null) != null))) | sort_by(.key | length) | last | .value.mcpServers.gbrain) // empty';
+
 export function generateBrainSyncBlock(ctx: TemplateContext): string {
   const isBrainHost = ctx.host === 'gbrain' || ctx.host === 'hermes';
   return `## Artifacts Sync (skill start)
@@ -79,10 +100,13 @@ _BRAIN_SYNC_MODE=$("$_BRAIN_CONFIG_BIN" get artifacts_sync_mode 2>/dev/null || e
 # Detect remote-MCP mode (Path 4 of /setup-gbrain). Local artifacts sync is
 # a no-op in remote mode; the brain server pulls from GitHub/GitLab on its
 # own cadence. Read claude.json directly to keep this preamble fast (no
-# subprocess to claude CLI on every skill start).
+# subprocess to claude CLI on every skill start). Both registration scopes
+# are read (#2499): user scope, then the nearest-ancestor project scope.
 _GBRAIN_MCP_MODE="none"
+_GBRAIN_MCP_ENTRY=""
 if command -v jq >/dev/null 2>&1 && [ -f "$HOME/.claude.json" ]; then
-  _GBRAIN_MCP_TYPE=$(jq -r '.mcpServers.gbrain.type // .mcpServers.gbrain.transport // empty' "$HOME/.claude.json" 2>/dev/null)
+  _GBRAIN_MCP_ENTRY=$(jq -c --arg cwd "$PWD" '${GBRAIN_MCP_ENTRY_JQ}' "$HOME/.claude.json" 2>/dev/null)
+  _GBRAIN_MCP_TYPE=$(printf '%s' "$_GBRAIN_MCP_ENTRY" | jq -r '.type // .transport // empty' 2>/dev/null)
   case "$_GBRAIN_MCP_TYPE" in
     url|http|sse) _GBRAIN_MCP_MODE="remote-http" ;;
     stdio) _GBRAIN_MCP_MODE="local-stdio" ;;
@@ -117,7 +141,7 @@ fi
 if [ "$_GBRAIN_MCP_MODE" = "remote-http" ]; then
   # Remote-MCP mode: local artifacts sync is a no-op (brain admin's server
   # pulls from GitHub/GitLab). Show the user this is by design, not broken.
-  _GBRAIN_HOST=$(jq -r '.mcpServers.gbrain.url // empty' "$HOME/.claude.json" 2>/dev/null | sed -E 's|^https?://([^/:]+).*|\\1|' | head -1 | tr -cd 'A-Za-z0-9._-')
+  _GBRAIN_HOST=$(printf '%s' "\${_GBRAIN_MCP_ENTRY:-}" | jq -r '.url // empty' 2>/dev/null | sed -E 's|^https?://([^/:]+).*|\\1|' | head -1 | tr -cd 'A-Za-z0-9._-')
   echo "ARTIFACTS_SYNC: remote-mode (managed by brain server \${_GBRAIN_HOST:-remote})"
 elif [ -d "$_GSTACK_HOME/.git" ] && [ "$_BRAIN_SYNC_MODE" != "off" ]; then
   _BRAIN_QUEUE_DEPTH=0
diff --git a/setup-browser-cookies/SKILL.md b/setup-browser-cookies/SKILL.md
index fb6a056ed..79f4d8809 100644
--- a/setup-browser-cookies/SKILL.md
+++ b/setup-browser-cookies/SKILL.md
@@ -375,10 +375,13 @@ _BRAIN_SYNC_MODE=$("$_BRAIN_CONFIG_BIN" get artifacts_sync_mode 2>/dev/null || e
 # Detect remote-MCP mode (Path 4 of /setup-gbrain). Local artifacts sync is
 # a no-op in remote mode; the brain server pulls from GitHub/GitLab on its
 # own cadence. Read claude.json directly to keep this preamble fast (no
-# subprocess to claude CLI on every skill start).
+# subprocess to claude CLI on every skill start). Both registration scopes
+# are read (#2499): user scope, then the nearest-ancestor project scope.
 _GBRAIN_MCP_MODE="none"
+_GBRAIN_MCP_ENTRY=""
 if command -v jq >/dev/null 2>&1 && [ -f "$HOME/.claude.json" ]; then
-  _GBRAIN_MCP_TYPE=$(jq -r '.mcpServers.gbrain.type // .mcpServers.gbrain.transport // empty' "$HOME/.claude.json" 2>/dev/null)
+  _GBRAIN_MCP_ENTRY=$(jq -c --arg cwd "$PWD" '.mcpServers.gbrain // ((.projects // {}) | to_entries | map(select((.key as $k | $cwd == $k or ($cwd | startswith($k + "/"))) and ((try .value.mcpServers.gbrain catch null) != null))) | sort_by(.key | length) | last | .value.mcpServers.gbrain) // empty' "$HOME/.claude.json" 2>/dev/null)
+  _GBRAIN_MCP_TYPE=$(printf '%s' "$_GBRAIN_MCP_ENTRY" | jq -r '.type // .transport // empty' 2>/dev/null)
   case "$_GBRAIN_MCP_TYPE" in
     url|http|sse) _GBRAIN_MCP_MODE="remote-http" ;;
     stdio) _GBRAIN_MCP_MODE="local-stdio" ;;
@@ -413,7 +416,7 @@ fi
 if [ "$_GBRAIN_MCP_MODE" = "remote-http" ]; then
   # Remote-MCP mode: local artifacts sync is a no-op (brain admin's server
   # pulls from GitHub/GitLab). Show the user this is by design, not broken.
-  _GBRAIN_HOST=$(jq -r '.mcpServers.gbrain.url // empty' "$HOME/.claude.json" 2>/dev/null | sed -E 's|^https?://([^/:]+).*|\1|' | head -1 | tr -cd 'A-Za-z0-9._-')
+  _GBRAIN_HOST=$(printf '%s' "${_GBRAIN_MCP_ENTRY:-}" | jq -r '.url // empty' 2>/dev/null | sed -E 's|^https?://([^/:]+).*|\1|' | head -1 | tr -cd 'A-Za-z0-9._-')
   echo "ARTIFACTS_SYNC: remote-mode (managed by brain server ${_GBRAIN_HOST:-remote})"
 elif [ -d "$_GSTACK_HOME/.git" ] && [ "$_BRAIN_SYNC_MODE" != "off" ]; then
   _BRAIN_QUEUE_DEPTH=0
diff --git a/setup-deploy/SKILL.md b/setup-deploy/SKILL.md
index d0b72575f..e4cb5b513 100644
--- a/setup-deploy/SKILL.md
+++ b/setup-deploy/SKILL.md
@@ -507,10 +507,13 @@ _BRAIN_SYNC_MODE=$("$_BRAIN_CONFIG_BIN" get artifacts_sync_mode 2>/dev/null || e
 # Detect remote-MCP mode (Path 4 of /setup-gbrain). Local artifacts sync is
 # a no-op in remote mode; the brain server pulls from GitHub/GitLab on its
 # own cadence. Read claude.json directly to keep this preamble fast (no
-# subprocess to claude CLI on every skill start).
+# subprocess to claude CLI on every skill start). Both registration scopes
+# are read (#2499): user scope, then the nearest-ancestor project scope.
 _GBRAIN_MCP_MODE="none"
+_GBRAIN_MCP_ENTRY=""
 if command -v jq >/dev/null 2>&1 && [ -f "$HOME/.claude.json" ]; then
-  _GBRAIN_MCP_TYPE=$(jq -r '.mcpServers.gbrain.type // .mcpServers.gbrain.transport // empty' "$HOME/.claude.json" 2>/dev/null)
+  _GBRAIN_MCP_ENTRY=$(jq -c --arg cwd "$PWD" '.mcpServers.gbrain // ((.projects // {}) | to_entries | map(select((.key as $k | $cwd == $k or ($cwd | startswith($k + "/"))) and ((try .value.mcpServers.gbrain catch null) != null))) | sort_by(.key | length) | last | .value.mcpServers.gbrain) // empty' "$HOME/.claude.json" 2>/dev/null)
+  _GBRAIN_MCP_TYPE=$(printf '%s' "$_GBRAIN_MCP_ENTRY" | jq -r '.type // .transport // empty' 2>/dev/null)
   case "$_GBRAIN_MCP_TYPE" in
     url|http|sse) _GBRAIN_MCP_MODE="remote-http" ;;
     stdio) _GBRAIN_MCP_MODE="local-stdio" ;;
@@ -545,7 +548,7 @@ fi
 if [ "$_GBRAIN_MCP_MODE" = "remote-http" ]; then
   # Remote-MCP mode: local artifacts sync is a no-op (brain admin's server
   # pulls from GitHub/GitLab). Show the user this is by design, not broken.
-  _GBRAIN_HOST=$(jq -r '.mcpServers.gbrain.url // empty' "$HOME/.claude.json" 2>/dev/null | sed -E 's|^https?://([^/:]+).*|\1|' | head -1 | tr -cd 'A-Za-z0-9._-')
+  _GBRAIN_HOST=$(printf '%s' "${_GBRAIN_MCP_ENTRY:-}" | jq -r '.url // empty' 2>/dev/null | sed -E 's|^https?://([^/:]+).*|\1|' | head -1 | tr -cd 'A-Za-z0-9._-')
   echo "ARTIFACTS_SYNC: remote-mode (managed by brain server ${_GBRAIN_HOST:-remote})"
 elif [ -d "$_GSTACK_HOME/.git" ] && [ "$_BRAIN_SYNC_MODE" != "off" ]; then
   _BRAIN_QUEUE_DEPTH=0
diff --git a/setup-gbrain/SKILL.md b/setup-gbrain/SKILL.md
index 54b3a987a..93a8cf4e1 100644
--- a/setup-gbrain/SKILL.md
+++ b/setup-gbrain/SKILL.md
@@ -506,10 +506,13 @@ _BRAIN_SYNC_MODE=$("$_BRAIN_CONFIG_BIN" get artifacts_sync_mode 2>/dev/null || e
 # Detect remote-MCP mode (Path 4 of /setup-gbrain). Local artifacts sync is
 # a no-op in remote mode; the brain server pulls from GitHub/GitLab on its
 # own cadence. Read claude.json directly to keep this preamble fast (no
-# subprocess to claude CLI on every skill start).
+# subprocess to claude CLI on every skill start). Both registration scopes
+# are read (#2499): user scope, then the nearest-ancestor project scope.
 _GBRAIN_MCP_MODE="none"
+_GBRAIN_MCP_ENTRY=""
 if command -v jq >/dev/null 2>&1 && [ -f "$HOME/.claude.json" ]; then
-  _GBRAIN_MCP_TYPE=$(jq -r '.mcpServers.gbrain.type // .mcpServers.gbrain.transport // empty' "$HOME/.claude.json" 2>/dev/null)
+  _GBRAIN_MCP_ENTRY=$(jq -c --arg cwd "$PWD" '.mcpServers.gbrain // ((.projects // {}) | to_entries | map(select((.key as $k | $cwd == $k or ($cwd | startswith($k + "/"))) and ((try .value.mcpServers.gbrain catch null) != null))) | sort_by(.key | length) | last | .value.mcpServers.gbrain) // empty' "$HOME/.claude.json" 2>/dev/null)
+  _GBRAIN_MCP_TYPE=$(printf '%s' "$_GBRAIN_MCP_ENTRY" | jq -r '.type // .transport // empty' 2>/dev/null)
   case "$_GBRAIN_MCP_TYPE" in
     url|http|sse) _GBRAIN_MCP_MODE="remote-http" ;;
     stdio) _GBRAIN_MCP_MODE="local-stdio" ;;
@@ -544,7 +547,7 @@ fi
 if [ "$_GBRAIN_MCP_MODE" = "remote-http" ]; then
   # Remote-MCP mode: local artifacts sync is a no-op (brain admin's server
   # pulls from GitHub/GitLab). Show the user this is by design, not broken.
-  _GBRAIN_HOST=$(jq -r '.mcpServers.gbrain.url // empty' "$HOME/.claude.json" 2>/dev/null | sed -E 's|^https?://([^/:]+).*|\1|' | head -1 | tr -cd 'A-Za-z0-9._-')
+  _GBRAIN_HOST=$(printf '%s' "${_GBRAIN_MCP_ENTRY:-}" | jq -r '.url // empty' 2>/dev/null | sed -E 's|^https?://([^/:]+).*|\1|' | head -1 | tr -cd 'A-Za-z0-9._-')
   echo "ARTIFACTS_SYNC: remote-mode (managed by brain server ${_GBRAIN_HOST:-remote})"
 elif [ -d "$_GSTACK_HOME/.git" ] && [ "$_BRAIN_SYNC_MODE" != "off" ]; then
   _BRAIN_QUEUE_DEPTH=0
diff --git a/ship/SKILL.md b/ship/SKILL.md
index 593b76f83..3ce2f8641 100644
--- a/ship/SKILL.md
+++ b/ship/SKILL.md
@@ -508,10 +508,13 @@ _BRAIN_SYNC_MODE=$("$_BRAIN_CONFIG_BIN" get artifacts_sync_mode 2>/dev/null || e
 # Detect remote-MCP mode (Path 4 of /setup-gbrain). Local artifacts sync is
 # a no-op in remote mode; the brain server pulls from GitHub/GitLab on its
 # own cadence. Read claude.json directly to keep this preamble fast (no
-# subprocess to claude CLI on every skill start).
+# subprocess to claude CLI on every skill start). Both registration scopes
+# are read (#2499): user scope, then the nearest-ancestor project scope.
 _GBRAIN_MCP_MODE="none"
+_GBRAIN_MCP_ENTRY=""
 if command -v jq >/dev/null 2>&1 && [ -f "$HOME/.claude.json" ]; then
-  _GBRAIN_MCP_TYPE=$(jq -r '.mcpServers.gbrain.type // .mcpServers.gbrain.transport // empty' "$HOME/.claude.json" 2>/dev/null)
+  _GBRAIN_MCP_ENTRY=$(jq -c --arg cwd "$PWD" '.mcpServers.gbrain // ((.projects // {}) | to_entries | map(select((.key as $k | $cwd == $k or ($cwd | startswith($k + "/"))) and ((try .value.mcpServers.gbrain catch null) != null))) | sort_by(.key | length) | last | .value.mcpServers.gbrain) // empty' "$HOME/.claude.json" 2>/dev/null)
+  _GBRAIN_MCP_TYPE=$(printf '%s' "$_GBRAIN_MCP_ENTRY" | jq -r '.type // .transport // empty' 2>/dev/null)
   case "$_GBRAIN_MCP_TYPE" in
     url|http|sse) _GBRAIN_MCP_MODE="remote-http" ;;
     stdio) _GBRAIN_MCP_MODE="local-stdio" ;;
@@ -546,7 +549,7 @@ fi
 if [ "$_GBRAIN_MCP_MODE" = "remote-http" ]; then
   # Remote-MCP mode: local artifacts sync is a no-op (brain admin's server
   # pulls from GitHub/GitLab). Show the user this is by design, not broken.
-  _GBRAIN_HOST=$(jq -r '.mcpServers.gbrain.url // empty' "$HOME/.claude.json" 2>/dev/null | sed -E 's|^https?://([^/:]+).*|\1|' | head -1 | tr -cd 'A-Za-z0-9._-')
+  _GBRAIN_HOST=$(printf '%s' "${_GBRAIN_MCP_ENTRY:-}" | jq -r '.url // empty' 2>/dev/null | sed -E 's|^https?://([^/:]+).*|\1|' | head -1 | tr -cd 'A-Za-z0-9._-')
   echo "ARTIFACTS_SYNC: remote-mode (managed by brain server ${_GBRAIN_HOST:-remote})"
 elif [ -d "$_GSTACK_HOME/.git" ] && [ "$_BRAIN_SYNC_MODE" != "off" ]; then
   _BRAIN_QUEUE_DEPTH=0
diff --git a/skillify/SKILL.md b/skillify/SKILL.md
index e22898eb5..e2a73c4d3 100644
--- a/skillify/SKILL.md
+++ b/skillify/SKILL.md
@@ -505,10 +505,13 @@ _BRAIN_SYNC_MODE=$("$_BRAIN_CONFIG_BIN" get artifacts_sync_mode 2>/dev/null || e
 # Detect remote-MCP mode (Path 4 of /setup-gbrain). Local artifacts sync is
 # a no-op in remote mode; the brain server pulls from GitHub/GitLab on its
 # own cadence. Read claude.json directly to keep this preamble fast (no
-# subprocess to claude CLI on every skill start).
+# subprocess to claude CLI on every skill start). Both registration scopes
+# are read (#2499): user scope, then the nearest-ancestor project scope.
 _GBRAIN_MCP_MODE="none"
+_GBRAIN_MCP_ENTRY=""
 if command -v jq >/dev/null 2>&1 && [ -f "$HOME/.claude.json" ]; then
-  _GBRAIN_MCP_TYPE=$(jq -r '.mcpServers.gbrain.type // .mcpServers.gbrain.transport // empty' "$HOME/.claude.json" 2>/dev/null)
+  _GBRAIN_MCP_ENTRY=$(jq -c --arg cwd "$PWD" '.mcpServers.gbrain // ((.projects // {}) | to_entries | map(select((.key as $k | $cwd == $k or ($cwd | startswith($k + "/"))) and ((try .value.mcpServers.gbrain catch null) != null))) | sort_by(.key | length) | last | .value.mcpServers.gbrain) // empty' "$HOME/.claude.json" 2>/dev/null)
+  _GBRAIN_MCP_TYPE=$(printf '%s' "$_GBRAIN_MCP_ENTRY" | jq -r '.type // .transport // empty' 2>/dev/null)
   case "$_GBRAIN_MCP_TYPE" in
     url|http|sse) _GBRAIN_MCP_MODE="remote-http" ;;
     stdio) _GBRAIN_MCP_MODE="local-stdio" ;;
@@ -543,7 +546,7 @@ fi
 if [ "$_GBRAIN_MCP_MODE" = "remote-http" ]; then
   # Remote-MCP mode: local artifacts sync is a no-op (brain admin's server
   # pulls from GitHub/GitLab). Show the user this is by design, not broken.
-  _GBRAIN_HOST=$(jq -r '.mcpServers.gbrain.url // empty' "$HOME/.claude.json" 2>/dev/null | sed -E 's|^https?://([^/:]+).*|\1|' | head -1 | tr -cd 'A-Za-z0-9._-')
+  _GBRAIN_HOST=$(printf '%s' "${_GBRAIN_MCP_ENTRY:-}" | jq -r '.url // empty' 2>/dev/null | sed -E 's|^https?://([^/:]+).*|\1|' | head -1 | tr -cd 'A-Za-z0-9._-')
   echo "ARTIFACTS_SYNC: remote-mode (managed by brain server ${_GBRAIN_HOST:-remote})"
 elif [ -d "$_GSTACK_HOME/.git" ] && [ "$_BRAIN_SYNC_MODE" != "off" ]; then
   _BRAIN_QUEUE_DEPTH=0
diff --git a/spec/SKILL.md b/spec/SKILL.md
index f51fa9aad..d0c0c8a3a 100644
--- a/spec/SKILL.md
+++ b/spec/SKILL.md
@@ -506,10 +506,13 @@ _BRAIN_SYNC_MODE=$("$_BRAIN_CONFIG_BIN" get artifacts_sync_mode 2>/dev/null || e
 # Detect remote-MCP mode (Path 4 of /setup-gbrain). Local artifacts sync is
 # a no-op in remote mode; the brain server pulls from GitHub/GitLab on its
 # own cadence. Read claude.json directly to keep this preamble fast (no
-# subprocess to claude CLI on every skill start).
+# subprocess to claude CLI on every skill start). Both registration scopes
+# are read (#2499): user scope, then the nearest-ancestor project scope.
 _GBRAIN_MCP_MODE="none"
+_GBRAIN_MCP_ENTRY=""
 if command -v jq >/dev/null 2>&1 && [ -f "$HOME/.claude.json" ]; then
-  _GBRAIN_MCP_TYPE=$(jq -r '.mcpServers.gbrain.type // .mcpServers.gbrain.transport // empty' "$HOME/.claude.json" 2>/dev/null)
+  _GBRAIN_MCP_ENTRY=$(jq -c --arg cwd "$PWD" '.mcpServers.gbrain // ((.projects // {}) | to_entries | map(select((.key as $k | $cwd == $k or ($cwd | startswith($k + "/"))) and ((try .value.mcpServers.gbrain catch null) != null))) | sort_by(.key | length) | last | .value.mcpServers.gbrain) // empty' "$HOME/.claude.json" 2>/dev/null)
+  _GBRAIN_MCP_TYPE=$(printf '%s' "$_GBRAIN_MCP_ENTRY" | jq -r '.type // .transport // empty' 2>/dev/null)
   case "$_GBRAIN_MCP_TYPE" in
     url|http|sse) _GBRAIN_MCP_MODE="remote-http" ;;
     stdio) _GBRAIN_MCP_MODE="local-stdio" ;;
@@ -544,7 +547,7 @@ fi
 if [ "$_GBRAIN_MCP_MODE" = "remote-http" ]; then
   # Remote-MCP mode: local artifacts sync is a no-op (brain admin's server
   # pulls from GitHub/GitLab). Show the user this is by design, not broken.
-  _GBRAIN_HOST=$(jq -r '.mcpServers.gbrain.url // empty' "$HOME/.claude.json" 2>/dev/null | sed -E 's|^https?://([^/:]+).*|\1|' | head -1 | tr -cd 'A-Za-z0-9._-')
+  _GBRAIN_HOST=$(printf '%s' "${_GBRAIN_MCP_ENTRY:-}" | jq -r '.url // empty' 2>/dev/null | sed -E 's|^https?://([^/:]+).*|\1|' | head -1 | tr -cd 'A-Za-z0-9._-')
   echo "ARTIFACTS_SYNC: remote-mode (managed by brain server ${_GBRAIN_HOST:-remote})"
 elif [ -d "$_GSTACK_HOME/.git" ] && [ "$_BRAIN_SYNC_MODE" != "off" ]; then
   _BRAIN_QUEUE_DEPTH=0
diff --git a/sync-gbrain/SKILL.md b/sync-gbrain/SKILL.md
index 48f003b22..89abd243e 100644
--- a/sync-gbrain/SKILL.md
+++ b/sync-gbrain/SKILL.md
@@ -507,10 +507,13 @@ _BRAIN_SYNC_MODE=$("$_BRAIN_CONFIG_BIN" get artifacts_sync_mode 2>/dev/null || e
 # Detect remote-MCP mode (Path 4 of /setup-gbrain). Local artifacts sync is
 # a no-op in remote mode; the brain server pulls from GitHub/GitLab on its
 # own cadence. Read claude.json directly to keep this preamble fast (no
-# subprocess to claude CLI on every skill start).
+# subprocess to claude CLI on every skill start). Both registration scopes
+# are read (#2499): user scope, then the nearest-ancestor project scope.
 _GBRAIN_MCP_MODE="none"
+_GBRAIN_MCP_ENTRY=""
 if command -v jq >/dev/null 2>&1 && [ -f "$HOME/.claude.json" ]; then
-  _GBRAIN_MCP_TYPE=$(jq -r '.mcpServers.gbrain.type // .mcpServers.gbrain.transport // empty' "$HOME/.claude.json" 2>/dev/null)
+  _GBRAIN_MCP_ENTRY=$(jq -c --arg cwd "$PWD" '.mcpServers.gbrain // ((.projects // {}) | to_entries | map(select((.key as $k | $cwd == $k or ($cwd | startswith($k + "/"))) and ((try .value.mcpServers.gbrain catch null) != null))) | sort_by(.key | length) | last | .value.mcpServers.gbrain) // empty' "$HOME/.claude.json" 2>/dev/null)
+  _GBRAIN_MCP_TYPE=$(printf '%s' "$_GBRAIN_MCP_ENTRY" | jq -r '.type // .transport // empty' 2>/dev/null)
   case "$_GBRAIN_MCP_TYPE" in
     url|http|sse) _GBRAIN_MCP_MODE="remote-http" ;;
     stdio) _GBRAIN_MCP_MODE="local-stdio" ;;
@@ -545,7 +548,7 @@ fi
 if [ "$_GBRAIN_MCP_MODE" = "remote-http" ]; then
   # Remote-MCP mode: local artifacts sync is a no-op (brain admin's server
   # pulls from GitHub/GitLab). Show the user this is by design, not broken.
-  _GBRAIN_HOST=$(jq -r '.mcpServers.gbrain.url // empty' "$HOME/.claude.json" 2>/dev/null | sed -E 's|^https?://([^/:]+).*|\1|' | head -1 | tr -cd 'A-Za-z0-9._-')
+  _GBRAIN_HOST=$(printf '%s' "${_GBRAIN_MCP_ENTRY:-}" | jq -r '.url // empty' 2>/dev/null | sed -E 's|^https?://([^/:]+).*|\1|' | head -1 | tr -cd 'A-Za-z0-9._-')
   echo "ARTIFACTS_SYNC: remote-mode (managed by brain server ${_GBRAIN_HOST:-remote})"
 elif [ -d "$_GSTACK_HOME/.git" ] && [ "$_BRAIN_SYNC_MODE" != "off" ]; then
   _BRAIN_QUEUE_DEPTH=0
diff --git a/test/brain-cache-roundtrip.test.ts b/test/brain-cache-roundtrip.test.ts
index 972708657..0466bd287 100644
--- a/test/brain-cache-roundtrip.test.ts
+++ b/test/brain-cache-roundtrip.test.ts
@@ -131,6 +131,59 @@ describe('brain-cache endpoint detection', () => {
     expect(typeof hash).toBe('string');
     expect(hash.length).toBeGreaterThan(0);
   });
+
+  // #2499: project-scoped registrations (.projects["/path"].mcpServers.gbrain)
+  // were never read — two different project-scoped brains both hashed to
+  // 'local', so switching between them never invalidated the cache.
+  test('detectEndpointHash resolves a project-scoped gbrain URL for a cwd inside the project (#2499)', async () => {
+    const mod = await importCache();
+    const cj = join(TMP_HOME, 'claude.json');
+    writeFileSync(cj, JSON.stringify({
+      projects: {
+        '/w/repo': { mcpServers: { gbrain: { type: 'http', url: 'https://a.example/mcp' } } },
+      },
+    }));
+    const inside = mod.detectEndpointHash(cj, '/w/repo/src/deep');
+    expect(inside).not.toBe('local');
+    expect(inside).toHaveLength(8);
+    // Path-boundary check: /w/repo2 is NOT inside /w/repo.
+    expect(mod.detectEndpointHash(cj, '/w/repo2')).toBe('local');
+  });
+
+  test('detectEndpointHash prefers the nearest-ancestor project entry (#2499)', async () => {
+    const mod = await importCache();
+    const cj = join(TMP_HOME, 'claude.json');
+    writeFileSync(cj, JSON.stringify({
+      projects: {
+        '/w/repo': { mcpServers: { gbrain: { url: 'https://outer.example/mcp' } } },
+        '/w/repo/nested': { mcpServers: { gbrain: { url: 'https://inner.example/mcp' } } },
+      },
+    }));
+    const inner = mod.detectEndpointHash(cj, '/w/repo/nested/sub');
+    const outer = mod.detectEndpointHash(cj, '/w/repo/other');
+    expect(inner).not.toBe(outer); // two brains → two hashes (the docstring scenario)
+    expect(inner).not.toBe('local');
+    expect(outer).not.toBe('local');
+  });
+
+  test('detectEndpointHash still prefers user scope over project scope (#2499)', async () => {
+    const mod = await importCache();
+    const cj = join(TMP_HOME, 'claude.json');
+    writeFileSync(cj, JSON.stringify({
+      mcpServers: { gbrain: { url: 'https://user.example/mcp' } },
+      projects: {
+        '/w/repo': { mcpServers: { gbrain: { url: 'https://proj.example/mcp' } } },
+      },
+    }));
+    const userScoped = mod.detectEndpointHash(cj, '/w/repo');
+    // Same file minus the user-scope entry → different hash proves user scope won.
+    writeFileSync(cj, JSON.stringify({
+      projects: {
+        '/w/repo': { mcpServers: { gbrain: { url: 'https://proj.example/mcp' } } },
+      },
+    }));
+    expect(mod.detectEndpointHash(cj, '/w/repo')).not.toBe(userScoped);
+  });
 });
 
 describe('brain-cache schema mismatch behavior', () => {
diff --git a/test/fixtures/golden/claude-ship-SKILL.md b/test/fixtures/golden/claude-ship-SKILL.md
index 593b76f83..3ce2f8641 100644
--- a/test/fixtures/golden/claude-ship-SKILL.md
+++ b/test/fixtures/golden/claude-ship-SKILL.md
@@ -508,10 +508,13 @@ _BRAIN_SYNC_MODE=$("$_BRAIN_CONFIG_BIN" get artifacts_sync_mode 2>/dev/null || e
 # Detect remote-MCP mode (Path 4 of /setup-gbrain). Local artifacts sync is
 # a no-op in remote mode; the brain server pulls from GitHub/GitLab on its
 # own cadence. Read claude.json directly to keep this preamble fast (no
-# subprocess to claude CLI on every skill start).
+# subprocess to claude CLI on every skill start). Both registration scopes
+# are read (#2499): user scope, then the nearest-ancestor project scope.
 _GBRAIN_MCP_MODE="none"
+_GBRAIN_MCP_ENTRY=""
 if command -v jq >/dev/null 2>&1 && [ -f "$HOME/.claude.json" ]; then
-  _GBRAIN_MCP_TYPE=$(jq -r '.mcpServers.gbrain.type // .mcpServers.gbrain.transport // empty' "$HOME/.claude.json" 2>/dev/null)
+  _GBRAIN_MCP_ENTRY=$(jq -c --arg cwd "$PWD" '.mcpServers.gbrain // ((.projects // {}) | to_entries | map(select((.key as $k | $cwd == $k or ($cwd | startswith($k + "/"))) and ((try .value.mcpServers.gbrain catch null) != null))) | sort_by(.key | length) | last | .value.mcpServers.gbrain) // empty' "$HOME/.claude.json" 2>/dev/null)
+  _GBRAIN_MCP_TYPE=$(printf '%s' "$_GBRAIN_MCP_ENTRY" | jq -r '.type // .transport // empty' 2>/dev/null)
   case "$_GBRAIN_MCP_TYPE" in
     url|http|sse) _GBRAIN_MCP_MODE="remote-http" ;;
     stdio) _GBRAIN_MCP_MODE="local-stdio" ;;
@@ -546,7 +549,7 @@ fi
 if [ "$_GBRAIN_MCP_MODE" = "remote-http" ]; then
   # Remote-MCP mode: local artifacts sync is a no-op (brain admin's server
   # pulls from GitHub/GitLab). Show the user this is by design, not broken.
-  _GBRAIN_HOST=$(jq -r '.mcpServers.gbrain.url // empty' "$HOME/.claude.json" 2>/dev/null | sed -E 's|^https?://([^/:]+).*|\1|' | head -1 | tr -cd 'A-Za-z0-9._-')
+  _GBRAIN_HOST=$(printf '%s' "${_GBRAIN_MCP_ENTRY:-}" | jq -r '.url // empty' 2>/dev/null | sed -E 's|^https?://([^/:]+).*|\1|' | head -1 | tr -cd 'A-Za-z0-9._-')
   echo "ARTIFACTS_SYNC: remote-mode (managed by brain server ${_GBRAIN_HOST:-remote})"
 elif [ -d "$_GSTACK_HOME/.git" ] && [ "$_BRAIN_SYNC_MODE" != "off" ]; then
   _BRAIN_QUEUE_DEPTH=0
diff --git a/test/fixtures/golden/codex-ship-SKILL.md b/test/fixtures/golden/codex-ship-SKILL.md
index 08eccf37a..8e4def16c 100644
--- a/test/fixtures/golden/codex-ship-SKILL.md
+++ b/test/fixtures/golden/codex-ship-SKILL.md
@@ -494,10 +494,13 @@ _BRAIN_SYNC_MODE=$("$_BRAIN_CONFIG_BIN" get artifacts_sync_mode 2>/dev/null || e
 # Detect remote-MCP mode (Path 4 of /setup-gbrain). Local artifacts sync is
 # a no-op in remote mode; the brain server pulls from GitHub/GitLab on its
 # own cadence. Read claude.json directly to keep this preamble fast (no
-# subprocess to claude CLI on every skill start).
+# subprocess to claude CLI on every skill start). Both registration scopes
+# are read (#2499): user scope, then the nearest-ancestor project scope.
 _GBRAIN_MCP_MODE="none"
+_GBRAIN_MCP_ENTRY=""
 if command -v jq >/dev/null 2>&1 && [ -f "$HOME/.claude.json" ]; then
-  _GBRAIN_MCP_TYPE=$(jq -r '.mcpServers.gbrain.type // .mcpServers.gbrain.transport // empty' "$HOME/.claude.json" 2>/dev/null)
+  _GBRAIN_MCP_ENTRY=$(jq -c --arg cwd "$PWD" '.mcpServers.gbrain // ((.projects // {}) | to_entries | map(select((.key as $k | $cwd == $k or ($cwd | startswith($k + "/"))) and ((try .value.mcpServers.gbrain catch null) != null))) | sort_by(.key | length) | last | .value.mcpServers.gbrain) // empty' "$HOME/.claude.json" 2>/dev/null)
+  _GBRAIN_MCP_TYPE=$(printf '%s' "$_GBRAIN_MCP_ENTRY" | jq -r '.type // .transport // empty' 2>/dev/null)
   case "$_GBRAIN_MCP_TYPE" in
     url|http|sse) _GBRAIN_MCP_MODE="remote-http" ;;
     stdio) _GBRAIN_MCP_MODE="local-stdio" ;;
@@ -532,7 +535,7 @@ fi
 if [ "$_GBRAIN_MCP_MODE" = "remote-http" ]; then
   # Remote-MCP mode: local artifacts sync is a no-op (brain admin's server
   # pulls from GitHub/GitLab). Show the user this is by design, not broken.
-  _GBRAIN_HOST=$(jq -r '.mcpServers.gbrain.url // empty' "$HOME/.claude.json" 2>/dev/null | sed -E 's|^https?://([^/:]+).*|\1|' | head -1 | tr -cd 'A-Za-z0-9._-')
+  _GBRAIN_HOST=$(printf '%s' "${_GBRAIN_MCP_ENTRY:-}" | jq -r '.url // empty' 2>/dev/null | sed -E 's|^https?://([^/:]+).*|\1|' | head -1 | tr -cd 'A-Za-z0-9._-')
   echo "ARTIFACTS_SYNC: remote-mode (managed by brain server ${_GBRAIN_HOST:-remote})"
 elif [ -d "$_GSTACK_HOME/.git" ] && [ "$_BRAIN_SYNC_MODE" != "off" ]; then
   _BRAIN_QUEUE_DEPTH=0
diff --git a/test/fixtures/golden/factory-ship-SKILL.md b/test/fixtures/golden/factory-ship-SKILL.md
index a954fcebf..d42534707 100644
--- a/test/fixtures/golden/factory-ship-SKILL.md
+++ b/test/fixtures/golden/factory-ship-SKILL.md
@@ -496,10 +496,13 @@ _BRAIN_SYNC_MODE=$("$_BRAIN_CONFIG_BIN" get artifacts_sync_mode 2>/dev/null || e
 # Detect remote-MCP mode (Path 4 of /setup-gbrain). Local artifacts sync is
 # a no-op in remote mode; the brain server pulls from GitHub/GitLab on its
 # own cadence. Read claude.json directly to keep this preamble fast (no
-# subprocess to claude CLI on every skill start).
+# subprocess to claude CLI on every skill start). Both registration scopes
+# are read (#2499): user scope, then the nearest-ancestor project scope.
 _GBRAIN_MCP_MODE="none"
+_GBRAIN_MCP_ENTRY=""
 if command -v jq >/dev/null 2>&1 && [ -f "$HOME/.claude.json" ]; then
-  _GBRAIN_MCP_TYPE=$(jq -r '.mcpServers.gbrain.type // .mcpServers.gbrain.transport // empty' "$HOME/.claude.json" 2>/dev/null)
+  _GBRAIN_MCP_ENTRY=$(jq -c --arg cwd "$PWD" '.mcpServers.gbrain // ((.projects // {}) | to_entries | map(select((.key as $k | $cwd == $k or ($cwd | startswith($k + "/"))) and ((try .value.mcpServers.gbrain catch null) != null))) | sort_by(.key | length) | last | .value.mcpServers.gbrain) // empty' "$HOME/.claude.json" 2>/dev/null)
+  _GBRAIN_MCP_TYPE=$(printf '%s' "$_GBRAIN_MCP_ENTRY" | jq -r '.type // .transport // empty' 2>/dev/null)
   case "$_GBRAIN_MCP_TYPE" in
     url|http|sse) _GBRAIN_MCP_MODE="remote-http" ;;
     stdio) _GBRAIN_MCP_MODE="local-stdio" ;;
@@ -534,7 +537,7 @@ fi
 if [ "$_GBRAIN_MCP_MODE" = "remote-http" ]; then
   # Remote-MCP mode: local artifacts sync is a no-op (brain admin's server
   # pulls from GitHub/GitLab). Show the user this is by design, not broken.
-  _GBRAIN_HOST=$(jq -r '.mcpServers.gbrain.url // empty' "$HOME/.claude.json" 2>/dev/null | sed -E 's|^https?://([^/:]+).*|\1|' | head -1 | tr -cd 'A-Za-z0-9._-')
+  _GBRAIN_HOST=$(printf '%s' "${_GBRAIN_MCP_ENTRY:-}" | jq -r '.url // empty' 2>/dev/null | sed -E 's|^https?://([^/:]+).*|\1|' | head -1 | tr -cd 'A-Za-z0-9._-')
   echo "ARTIFACTS_SYNC: remote-mode (managed by brain server ${_GBRAIN_HOST:-remote})"
 elif [ -d "$_GSTACK_HOME/.git" ] && [ "$_BRAIN_SYNC_MODE" != "off" ]; then
   _BRAIN_QUEUE_DEPTH=0
diff --git a/test/gen-skill-docs.test.ts b/test/gen-skill-docs.test.ts
index b69b104e5..259ce1f1d 100644
--- a/test/gen-skill-docs.test.ts
+++ b/test/gen-skill-docs.test.ts
@@ -3604,3 +3604,83 @@ describe('PREAMBLE resolution requires declared preamble-tier', () => {
     expect(offenders).toEqual([]);
   });
 });
+
+// ---------------------------------------------------------------------------
+// #2499: gbrain MCP detection must read BOTH ~/.claude.json scopes.
+// Claude Code registers MCP servers at user scope (.mcpServers) and project
+// scope (.projects["/abs/path"].mcpServers — what `claude mcp add` without
+// --scope user writes). The rendered brain-sync block previously read only
+// user scope, so a correctly configured project-scoped brain was invisible.
+// ---------------------------------------------------------------------------
+describe('brain-sync block reads project-scoped MCP registrations (#2499)', () => {
+  const rendered = fs.readFileSync(path.join(ROOT, 'SKILL.md'), 'utf-8');
+
+  test('rendered _GBRAIN_MCP_ENTRY jq resolves project scope with nearest-ancestor cwd match', () => {
+    const line = rendered.split('\n').find((l) => l.includes('_GBRAIN_MCP_ENTRY=$('));
+    expect(line).toBeDefined();
+    // Project-scope read present, driven by $PWD.
+    expect(line!).toContain('--arg cwd "$PWD"');
+    expect(line!).toContain('.projects');
+    // User scope still resolved first.
+    expect(line!).toContain('.mcpServers.gbrain');
+    // The old user-scope-only filter is gone from the rendered output.
+    expect(rendered).not.toContain('.mcpServers.gbrain.type // .mcpServers.gbrain.transport');
+    expect(rendered).not.toContain(".mcpServers.gbrain.url // empty");
+  });
+
+  test('rendered _GBRAIN_MCP_TYPE and _GBRAIN_HOST extract from the resolved entry', () => {
+    const typeLine = rendered.split('\n').find((l) => l.includes('_GBRAIN_MCP_TYPE=$('));
+    const hostLine = rendered.split('\n').find((l) => l.includes('_GBRAIN_HOST=$('));
+    expect(typeLine).toBeDefined();
+    expect(hostLine).toBeDefined();
+    expect(typeLine!).toContain('_GBRAIN_MCP_ENTRY');
+    expect(hostLine!).toContain('_GBRAIN_MCP_ENTRY');
+  });
+
+  test('rendered jq lines FUNCTION: project-scoped registration resolves for a cwd inside the project', () => {
+    // Execute the exact rendered bytes, not a re-derivation: extract the
+    // _GBRAIN_MCP_ENTRY + _GBRAIN_MCP_TYPE lines from the generated SKILL.md
+    // and run them in bash against a fixture ~/.claude.json that carries ONLY
+    // a project-scoped gbrain registration.
+    const lines = rendered.split('\n');
+    const entryLine = lines.find((l) => l.includes('_GBRAIN_MCP_ENTRY=$('));
+    const typeLine = lines.find((l) => l.includes('_GBRAIN_MCP_TYPE=$('));
+    expect(entryLine).toBeDefined();
+    expect(typeLine).toBeDefined();
+
+    const tmpHome = fs.mkdtempSync(path.join(os.tmpdir(), 'gstack-2499-home-'));
+    const projectDir = fs.mkdtempSync(path.join(os.tmpdir(), 'gstack-2499-proj-'));
+    const nestedCwd = path.join(projectDir, 'src', 'deep');
+    fs.mkdirSync(nestedCwd, { recursive: true });
+    try {
+      fs.writeFileSync(
+        path.join(tmpHome, '.claude.json'),
+        JSON.stringify({
+          projects: {
+            [projectDir]: {
+              mcpServers: { gbrain: { type: 'http', url: 'https://brain.example.com/mcp' } },
+            },
+          },
+        }),
+      );
+      const script = `cd "$1" || exit 1\n${entryLine!.trim()}\n${typeLine!.trim()}\necho "RESOLVED:$_GBRAIN_MCP_TYPE"`;
+      const r = spawnSync('bash', ['-c', script, 'bash', nestedCwd], {
+        encoding: 'utf-8',
+        env: { ...process.env, HOME: tmpHome },
+        timeout: 10_000,
+      });
+      expect(r.stdout).toContain('RESOLVED:http');
+
+      // Discriminator: a cwd OUTSIDE the project must NOT resolve it.
+      const outside = spawnSync('bash', ['-c', script, 'bash', os.tmpdir()], {
+        encoding: 'utf-8',
+        env: { ...process.env, HOME: tmpHome },
+        timeout: 10_000,
+      });
+      expect(outside.stdout).toContain('RESOLVED:\n');
+    } finally {
+      fs.rmSync(tmpHome, { recursive: true, force: true });
+      fs.rmSync(projectDir, { recursive: true, force: true });
+    }
+  });
+});
diff --git a/test/helpers/carve-guards.ts b/test/helpers/carve-guards.ts
index 40664b651..871acf0fb 100644
--- a/test/helpers/carve-guards.ts
+++ b/test/helpers/carve-guards.ts
@@ -181,7 +181,9 @@ export const CARVE_GUARDS: Record<string, CarveGuard> = {
     // v1.65 merge: provisional larger-of-both-waves budget; re-measured below.
         // Fork port wave 2 (#703): the repo-doc-preference block in the design
     // check grew every plan-review skeleton ~0.7KB. Measured values noted.
-    maxSkeletonBytes: 70_000, // measured 68,780
+    // #2499 project-scope MCP jq in the brain-sync block grew every tier-2+
+    // skeleton ~1.5KB (entry resolution emitted once per SKILL.md).
+    maxSkeletonBytes: 70_500, // measured 70,318
     minUnionBytes: 70_000,
     mustContain: ['Architecture', 'Code Quality', 'Test', 'Performance'],
     // Cross-cutting preamble growth (v1.57.2.0 AUQ-failure prose fallback + the
@@ -236,7 +238,9 @@ export const CARVE_GUARDS: Record<string, CarveGuard> = {
     // v1.2.0 activation lift: first-run-guidance section in the shared preamble.
         // Fork port wave 2 (#703): the repo-doc-preference block in the design
     // check grew every plan-review skeleton ~0.7KB. Measured values noted.
-    maxSkeletonBytes: 82_000, // measured 80,493
+    // #2499 project-scope MCP jq in the brain-sync block grew every tier-2+
+    // skeleton ~1.5KB (entry resolution emitted once per SKILL.md).
+    maxSkeletonBytes: 82_500, // measured 82,031
     minUnionBytes: 70_000,
     mustContain: ['developer experience', 'Getting Started'],
     // Default-on Codex outside-voice (codexPreflight block + CODEX_MODE branch
@@ -264,7 +268,9 @@ export const CARVE_GUARDS: Record<string, CarveGuard> = {
     // (judgment must be visible before the workflow directs the user to a
     // vendor site), plus the #703 dual-write + repo-doc-preference block and
     // the #538 opt-out + D1 evidence directive — ratio 1.104 measured.
-    maxSkeletonBytes: 101_000,
+    // #2499 project-scope MCP jq in the brain-sync block grew every tier-2+
+    // skeleton ~1.5KB (entry resolution emitted once per SKILL.md).
+    maxSkeletonBytes: 101_500, // measured 101,314
     minUnionBytes: 70_000,
     mustContain: ['design doc', 'problem statement'],
     maxSizeRatio: 1.12,