fix: resolve GBRAIN_HOME with gbrain's parent-dir semantics (#2521)

gstack treated GBRAIN_HOME as the config directory; gbrain's configDir()
treats it as the PARENT and always appends `.gbrain` itself (the contract
is explicit in gbrain's source: GBRAIN_HOME=/tmp/x → /tmp/x/.gbrain/
config.json). With GBRAIN_HOME set, gstack classified engine status from
a file gbrain never reads — the probe's two halves (file checks vs the
spawned `gbrain sources list`) looked at DIFFERENT installs, so any
resulting status was arbitrary: missing-config/broken-config against
healthy installs, or a thin-client marker gstack saw that gbrain itself
reported as "No brain configured".

New shared resolver `gbrainConfigDir()` in lib/gbrain-exec.ts is the
single source of truth. All seven gstack sites route through the contract:

- lib/gbrain-local-status.ts gbrainConfigPath (the classifier's file half)
- bin/gstack-gbrain-detect GBRAIN_CONFIG + readRemoteMcpUrl
- lib/gbrain-exec.ts buildGbrainEnv (the probe's DATABASE_URL seed —
  fixing only the classifier would have left the split-brain in the
  spawn half, flagged by the reporter)
- lib/gbrain-guards.ts gbrainHome (clones-dir + autopilot-lock paths)
- lib/gstack-memory-helpers.ts gbrainConfigPath (engine-tier fallback)
- bin/gstack-gbrain-install pre-doctor config check (shell)

Unit tests cover GBRAIN_HOME set (config found at $GBRAIN_HOME/.gbrain),
the old flat layout explicitly NOT read (both classifier and
buildGbrainEnv), and unset (~/.gbrain unchanged). Existing fixtures that
encoded the deviant flat layout are updated to gbrain's contract.

Root-cause analysis by @d-danielsun in #2521.

Deviation from the 3-site plan spec: the same deviant resolution existed
in four more sites (buildGbrainEnv, gbrain-guards, memory-helpers,
gbrain-install); fixing only three would have left gstack disagreeing
with itself as well as with gbrain, so the whole class moved to the
shared resolver in one change.

Fixes #2521

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

bin/gstack-gbrain-detect

@@ -43,18 +43,17 @@ import {
   resolveGbrainBin,
   readGbrainVersion,
 } from "../lib/gbrain-local-status";
-import { isTransactionModePooler } from "../lib/gbrain-exec";
+import { gbrainConfigDir, isTransactionModePooler } from "../lib/gbrain-exec";
 
 const STATE_DIR = process.env.GSTACK_HOME || join(userHome(), ".gstack");
 const SCRIPT_DIR = __dirname;
 const CONFIG_BIN = join(SCRIPT_DIR, "gstack-config");
-// Honors GBRAIN_HOME — must stay consistent with lib/gbrain-local-status's
+// Honors GBRAIN_HOME with gbrain's own configDir() semantics (#2521:
-// config resolution, or the detect JSON reports gbrain_local_status "ok"
+// GBRAIN_HOME is a parent dir, `.gbrain` is appended) — must stay consistent
-// alongside gbrain_config_exists false for relocated-home users.
+// with lib/gbrain-local-status's config resolution, or the detect JSON
-const GBRAIN_CONFIG = join(
+// reports gbrain_local_status "ok" alongside gbrain_config_exists false for
-  process.env.GBRAIN_HOME || join(userHome(), ".gbrain"),
+// relocated-home users. Both route through gbrainConfigDir.
-  "config.json",
+const GBRAIN_CONFIG = join(gbrainConfigDir(), "config.json");
-);
 const CLAUDE_JSON = join(userHome(), ".claude.json");
 
 function userHome(): string {
@@ -232,8 +231,7 @@ function detectMcpMode(): "local-stdio" | "remote-http" | "none" {
 
 /** remote_mcp.mcp_url from gbrain's own config (thin-client marker, #2051). */
 function readRemoteMcpUrl(): string {
-  const gbrainHome = process.env.GBRAIN_HOME || join(userHome(), ".gbrain");
+  const cfg = tryReadJSON(join(gbrainConfigDir(), "config.json")) as
-  const cfg = tryReadJSON(join(gbrainHome, "config.json")) as
     | { remote_mcp?: { mcp_url?: string } }
     | null;
   return cfg?.remote_mcp?.mcp_url || "";

bin/gstack-gbrain-install

@@ -235,7 +235,14 @@ fi
 # a hard gate so a broken gbrain is caught at setup, not at data-loss time.
 # Pre-init installs skip this (config not written yet); the full
 # `/sync-gbrain --dry-run` self-test runs from /setup-gbrain after `gbrain init`.
-_GBRAIN_HOME_CHECK="${GBRAIN_HOME:-$HOME/.gbrain}"
+# #2521: GBRAIN_HOME is a PARENT dir per gbrain's configDir() contract —
+# gbrain appends `.gbrain` itself, so the config lives at
+# $GBRAIN_HOME/.gbrain/config.json (or ~/.gbrain/config.json when unset).
+if [ -n "${GBRAIN_HOME:-}" ]; then
+  _GBRAIN_HOME_CHECK="$GBRAIN_HOME/.gbrain"
+else
+  _GBRAIN_HOME_CHECK="$HOME/.gbrain"
+fi
 if [ -f "$_GBRAIN_HOME_CHECK/config.json" ]; then
   if ! gbrain doctor --fast >/dev/null 2>&1; then
     echo "" >&2

lib/gbrain-exec.ts

@@ -21,10 +21,12 @@
  *      spawn. This is the central bug the helper exists to prevent
  *      regressing on.
  *
- *   3. **`GBRAIN_HOME` honored consistently.** Other gstack helpers
+ *   3. **`GBRAIN_HOME` honored consistently — with gbrain's own semantics
- *      (`detectEngineTier`) already honor `GBRAIN_HOME`. `buildGbrainEnv`
+ *      (#2521).** gbrain's configDir() treats `GBRAIN_HOME` as a PARENT
- *      reads from `${GBRAIN_HOME:-$HOME/.gbrain}/config.json` so all
+ *      directory and always appends `.gbrain` itself (GBRAIN_HOME=/tmp/x
- *      gstack-side gbrain calls agree on which config file matters.
+ *      → /tmp/x/.gbrain/config.json). Every gstack-side read goes through
+ *      `gbrainConfigDir()` below so gstack and gbrain agree on which
+ *      config file matters.
  *
  * **Escape hatch:** `GSTACK_RESPECT_ENV_DATABASE_URL=1` returns the
  * caller's env unchanged. Use only when the brain intentionally lives in
@@ -75,8 +77,21 @@ export function isTransactionModePooler(url: string): boolean {
 }
 
 /**
- * Build an env dict with DATABASE_URL seeded from
+ * gbrain's config directory, matching gbrain's own configDir() contract
- * `${GBRAIN_HOME:-$HOME/.gbrain}/config.json`. Returns the base env
+ * (#2521): `GBRAIN_HOME` is a PARENT directory — gbrain always appends
+ * `.gbrain` itself, so GBRAIN_HOME=/tmp/x reads /tmp/x/.gbrain/config.json.
+ * Unset → ~/.gbrain. Every gstack-side gbrain-config read MUST resolve
+ * through this helper, or gstack classifies engine status from a file
+ * gbrain never reads.
+ */
+export function gbrainConfigDir(env: NodeJS.ProcessEnv = process.env): string {
+  if (env.GBRAIN_HOME) return join(env.GBRAIN_HOME, ".gbrain");
+  return join(env.HOME || homedir(), ".gbrain");
+}
+
+/**
+ * Build an env dict with DATABASE_URL seeded from gbrain's config.json
+ * (resolved via `gbrainConfigDir`). Returns the base env
  * unchanged when:
  *   - `GSTACK_RESPECT_ENV_DATABASE_URL=1` (intentional opt-out),
  *   - the config file is missing or unparseable,
@@ -98,9 +113,7 @@ export function buildGbrainEnv(opts: BuildGbrainEnvOptions = {}): NodeJS.Process
   const out: NodeJS.ProcessEnv = { ...baseEnv };
   if (baseEnv.GSTACK_RESPECT_ENV_DATABASE_URL === "1") return out;
 
-  const homeBase = baseEnv.HOME || homedir();
+  const configPath = join(gbrainConfigDir(baseEnv), "config.json");
-  const gbrainHome = baseEnv.GBRAIN_HOME || join(homeBase, ".gbrain");
-  const configPath = join(gbrainHome, "config.json");
   if (!existsSync(configPath)) return out;
 
   let cfg: GbrainConfig = {};

lib/gbrain-guards.ts

@@ -36,7 +36,9 @@ import { execGbrainJson, execGbrainText, NEEDS_SHELL_ON_WINDOWS } from "./gbrain
 import { parseSourcesList, type GbrainSourceRow } from "./gbrain-sources";
 
 export function gbrainHome(env: NodeJS.ProcessEnv = process.env): string {
-  return env.GBRAIN_HOME || join(homedir(), ".gbrain");
+  // #2521: GBRAIN_HOME is a PARENT dir per gbrain's configDir() contract —
+  // gbrain appends `.gbrain` itself, so gstack must too.
+  return env.GBRAIN_HOME ? join(env.GBRAIN_HOME, ".gbrain") : join(homedir(), ".gbrain");
 }
 
 /**

lib/gbrain-local-status.ts

@@ -48,7 +48,7 @@ import {
 import { atomicWriteSync } from "./fs-atomic";
 import { homedir } from "os";
 import { dirname, join } from "path";
-import { buildGbrainEnv, NEEDS_SHELL_ON_WINDOWS } from "./gbrain-exec";
+import { buildGbrainEnv, gbrainConfigDir, NEEDS_SHELL_ON_WINDOWS } from "./gbrain-exec";
 
 export type LocalEngineStatus =
   | "ok"
@@ -122,11 +122,14 @@ export function cacheFilePath(): string {
   );
 }
 
-/** Honors GBRAIN_HOME (codex D11) — same resolution as buildGbrainEnv. */
+/**
+ * Honors GBRAIN_HOME (codex D11) with gbrain's own configDir() semantics
+ * (#2521): GBRAIN_HOME is a parent dir, `.gbrain` is appended. Same
+ * resolution as buildGbrainEnv — both route through gbrainConfigDir.
+ */
 function gbrainConfigPath(env?: NodeJS.ProcessEnv): string {
   const e = env ?? process.env;
-  const gbrainHome = e.GBRAIN_HOME || join(userHome(e), ".gbrain");
+  return join(gbrainConfigDir(e), "config.json");
-  return join(gbrainHome, "config.json");
 }
 
 /**

lib/gstack-memory-helpers.ts

@@ -19,6 +19,7 @@
 
 import { existsSync, readFileSync, writeFileSync, mkdirSync, statSync } from "fs";
 import { appendJsonl } from "./jsonl-store";
+import { gbrainConfigDir } from "./gbrain-exec";
 import { dirname, join } from "path";
 import { execFileSync } from "child_process";
 import { homedir } from "os";
@@ -256,12 +257,13 @@ export function detectEngineTier(): EngineDetect {
 }
 
 // Returns gbrain's config.json path, honoring GBRAIN_HOME env var with a
-// fallback to ~/.gbrain. gbrain >=0.25 dropped the top-level `engine` field
+// fallback to ~/.gbrain. Resolution matches gbrain's own configDir()
+// contract (#2521): GBRAIN_HOME is a parent dir, `.gbrain` is appended.
+// gbrain >=0.25 dropped the top-level `engine` field
 // from doctor output, so this file is the only reliable source for engine
 // detection on that version. See #1415.
 function gbrainConfigPath(): string {
-  const root = process.env.GBRAIN_HOME || join(homedir(), ".gbrain");
+  return join(gbrainConfigDir(process.env), "config.json");
-  return join(root, "config.json");
 }
 
 // Best-effort JSONL append to ~/.gstack/.gbrain-errors.jsonl. Never throws.

test/build-gbrain-env.test.ts

@@ -77,17 +77,34 @@ describe("buildGbrainEnv", () => {
     expect(result.DATABASE_URL).toBe("postgresql://app/db");
   });
 
-  it("honors GBRAIN_HOME when set (config aligned with detectEngineTier)", () => {
+  it("honors GBRAIN_HOME when set, with gbrain's parent-dir semantics (#2521)", () => {
-    // Move the config to an alternate dir; set GBRAIN_HOME to point at it.
+    // Move the config to an alternate dir; set GBRAIN_HOME to point at its
+    // PARENT — gbrain's configDir() appends `.gbrain` itself, so
+    // GBRAIN_HOME=/x reads /x/.gbrain/config.json.
     const altGbrainHome = join(home, "alt-gbrain");
-    mkdirSync(altGbrainHome, { recursive: true });
+    mkdirSync(join(altGbrainHome, ".gbrain"), { recursive: true });
-    writeFileSync(join(altGbrainHome, "config.json"), JSON.stringify({ database_url: "postgresql://alt/db" }));
+    writeFileSync(
+      join(altGbrainHome, ".gbrain", "config.json"),
+      JSON.stringify({ database_url: "postgresql://alt/db" }),
+    );
     // No file at the default ~/.gbrain location.
     const baseEnv = { HOME: home, GBRAIN_HOME: altGbrainHome };
     const result = buildGbrainEnv({ baseEnv });
     expect(result.DATABASE_URL).toBe("postgresql://alt/db");
   });
 
+  it("ignores a config at $GBRAIN_HOME/config.json — gbrain never reads that file (#2521)", () => {
+    const altGbrainHome = join(home, "alt-gbrain-flat");
+    mkdirSync(altGbrainHome, { recursive: true });
+    writeFileSync(
+      join(altGbrainHome, "config.json"),
+      JSON.stringify({ database_url: "postgresql://alt/db" }),
+    );
+    const baseEnv = { HOME: home, GBRAIN_HOME: altGbrainHome };
+    const result = buildGbrainEnv({ baseEnv });
+    expect(result.DATABASE_URL).toBeUndefined();
+  });
+
   it("returns a fresh env object — never the caller's env by identity", () => {
     // Codex review #11: object-identity equality lets later mutation of the
     // returned env leak back into the caller's view. The helper MUST clone.

test/code-intelligence.test.ts

@@ -953,7 +953,9 @@ exit 1
       ...process.env,
       GSTACK_HOME: home,
       HOME: home,
-      GBRAIN_HOME: gbrainHome,
+      // #2521: GBRAIN_HOME is the PARENT of .gbrain per gbrain's configDir()
+      // contract — pointing it at `home` resolves to home/.gbrain/config.json.
+      GBRAIN_HOME: home,
       PATH: `${shimDir}:${process.env.PATH}`,
       // Dead loopback port → the Sourcebot probe fails fast + deterministically
       // (connection refused) instead of poking whatever operator dev server

test/gbrain-local-status.test.ts

@@ -269,20 +269,46 @@ describe("lib/gbrain-local-status — status classification", () => {
     expect(localEngineStatus({ noCache: true })).toBe("timeout");
   });
 
-  it("honors GBRAIN_HOME for config detection (codex D11)", () => {
+  it("honors GBRAIN_HOME for config detection (codex D11) with gbrain's parent-dir semantics (#2521)", () => {
-    // Config lives ONLY at the alternate GBRAIN_HOME; ~/.gbrain has none.
+    // Config lives ONLY under the alternate GBRAIN_HOME; ~/.gbrain has none.
+    // gbrain's configDir() treats GBRAIN_HOME as a PARENT dir and appends
+    // `.gbrain` itself: GBRAIN_HOME=/x → /x/.gbrain/config.json.
     env = makeEnv({ withGbrain: true, gbrainBehavior: "ok", withConfig: false });
     restoreEnv = applyEnv(env);
     const altHome = join(env.tmp, "alt-gbrain");
+    mkdirSync(join(altHome, ".gbrain"), { recursive: true });
+    writeFileSync(
+      join(altHome, ".gbrain", "config.json"),
+      JSON.stringify({ engine: "pglite", database_url: "pglite:///fake" }),
+    );
+    // Without GBRAIN_HOME: misclassified as missing-config.
+    expect(localEngineStatus({ noCache: true })).toBe("missing-config");
+    // With GBRAIN_HOME: the relocated config is found at $GBRAIN_HOME/.gbrain.
+    process.env.GBRAIN_HOME = altHome;
+    expect(localEngineStatus({ noCache: true })).toBe("ok");
+  });
+
+  it("does NOT read $GBRAIN_HOME/config.json directly — gbrain never reads that file (#2521)", () => {
+    // A config placed at gstack's OLD (wrong) resolution must be invisible:
+    // gbrain itself would report "No brain configured" for this layout, so
+    // gstack classifying "ok" from it is the #2521 split-brain.
+    env = makeEnv({ withGbrain: true, gbrainBehavior: "ok", withConfig: false });
+    restoreEnv = applyEnv(env);
+    const altHome = join(env.tmp, "alt-gbrain-flat");
     mkdirSync(altHome, { recursive: true });
     writeFileSync(
       join(altHome, "config.json"),
       JSON.stringify({ engine: "pglite", database_url: "pglite:///fake" }),
     );
-    // Without GBRAIN_HOME: misclassified as missing-config.
-    expect(localEngineStatus({ noCache: true })).toBe("missing-config");
-    // With GBRAIN_HOME: the relocated config is found.
     process.env.GBRAIN_HOME = altHome;
+    expect(localEngineStatus({ noCache: true })).toBe("missing-config");
+  });
+
+  it("with GBRAIN_HOME unset, config resolution stays at ~/.gbrain (#2521 unset half)", () => {
+    env = makeEnv({ withGbrain: true, gbrainBehavior: "ok", withConfig: true });
+    restoreEnv = applyEnv(env);
+    // applyEnv deletes GBRAIN_HOME; config was written at $HOME/.gbrain.
+    expect(process.env.GBRAIN_HOME).toBeUndefined();
     expect(localEngineStatus({ noCache: true })).toBe("ok");
   });
 });

test/gstack-memory-helpers.test.ts

@@ -462,10 +462,13 @@ describe("detectEngineTier", () => {
     // Regression test for #1415: gbrain >=0.25 doctor output dropped the
     // top-level `engine` field. The detect path must fall back to config.json.
     // We force the doctor call to fail (PATH stripped of gbrain) and write a
-    // synthetic config to GBRAIN_HOME so the fallback path is deterministic.
+    // synthetic config under GBRAIN_HOME so the fallback path is
+    // deterministic. Per gbrain's configDir() contract (#2521), GBRAIN_HOME
+    // is a parent dir — the config lives at $GBRAIN_HOME/.gbrain/config.json.
     process.env.PATH = "/nonexistent-no-gbrain-here";
+    mkdirSync(join(testGbrainHome, ".gbrain"), { recursive: true });
     writeFileSync(
-      join(testGbrainHome, "config.json"),
+      join(testGbrainHome, ".gbrain", "config.json"),
       JSON.stringify({ engine: "postgres", database_url: "postgresql://test/example" }),
       "utf-8"
     );
@@ -500,8 +503,9 @@ exit 0
       { mode: 0o755 }
     );
     process.env.PATH = `${binDir}:${process.env.PATH || ""}`;
+    mkdirSync(join(testGbrainHome, ".gbrain"), { recursive: true });
     writeFileSync(
-      join(testGbrainHome, "config.json"),
+      join(testGbrainHome, ".gbrain", "config.json"),
       JSON.stringify({ engine: "pglite" }),
       "utf-8"
     );