fix: read project-scoped MCP registrations in gbrain detection (#2499)

Claude Code registers MCP servers at two scopes in ~/.claude.json: user
scope (.mcpServers) and project scope (.projects["/abs/path"].mcpServers
— what `claude mcp add` WITHOUT --scope user writes). Every gbrain
detection site read only user scope, so a correctly configured
project-scoped brain was invisible: brain-aware blocks suppressed,
remote-mode artifacts sync never recognised, and detectEndpointHash fell
through to the 'local' literal — two different project-scoped brains
hashed identically, so switching between them never invalidated the
cache, the exact scenario the function's docstring says it exists to
catch. Nothing errored; the features just quietly were not there.

Two sites fixed:

- scripts/resolvers/preamble/generate-brain-sync-block.ts: the shared
  detection block (rendered into every tier-2+ SKILL.md) now resolves the
  gbrain entry ONCE into _GBRAIN_MCP_ENTRY — 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: /a/repo never
  matches /a/repo2; a nested project WITHOUT gbrain doesn't shadow its
  parent's registration). _GBRAIN_MCP_TYPE and _GBRAIN_HOST extract from
  the resolved entry, so claude.json is parsed once per skill start. All
  SKILL.md files regenerated in this commit; the ship golden fixtures and
  three carve-guard skeleton caps (plan-eng-review, plan-devex-review,
  office-hours; ~1.5KB rendered growth per skill) are refreshed with
  measured values.
- bin/gstack-brain-cache detectEndpointHash: same resolution order in TS
  (user scope, else nearest-ancestor project entry by cwd, both path
  separators for Windows keys).

Tests: rendered-output tests in test/gen-skill-docs.test.ts pin the
regenerated block (static markers + a FUNCTIONAL run of the exact
rendered lines against a fixture ~/.claude.json with only a
project-scoped registration, plus an outside-cwd discriminator);
detectEndpointHash unit tests in test/brain-cache-roundtrip.test.ts cover
project-scope resolve, path-boundary, nearest-ancestor distinct hashes,
and user-scope precedence.

Root-cause analysis by @samporter-31 in #2499.

Fixes #2499

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

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

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

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

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

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)
 // ──────────────────────────────────────────────────────────────────────────

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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', () => {

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

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

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

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 });
+    }
+  });
+});

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,