@aroman22/codegraph-vba-darwin-arm64 1.5.2 → 1.6.1

package/lib/dist/sync/worktree.d.ts

@@ -25,6 +25,15 @@
  * is exactly the distinction this module relies on.
  */
 export declare function gitWorktreeRoot(dir: string): string | null;
+/**
+ * Absolute, symlink-resolved git **common** directory for `dir` — the shared
+ * `.git` that all worktrees of one repository point at. Linked worktrees of the
+ * same repo report the SAME common dir; a submodule or an embedded clone is a
+ * DIFFERENT repository and reports its own (`…/.git/modules/<name>` or its own
+ * `.git`). That distinction is what separates a genuine "borrowed worktree"
+ * from a nested repo the parent index already covers. Null when not a repo.
+ */
+export declare function gitCommonDir(dir: string): string | null;
 export interface WorktreeIndexMismatch {
     /** The git working tree the command was run from. */
     worktreeRoot: string;

package/lib/dist/sync/worktree.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"worktree.d.ts","sourceRoot":"","sources":["../../src/sync/worktree.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;;GAiBG;AAMH;;;;;;;GAOG;AACH,wBAAgB,eAAe,CAAC,GAAG,EAAE,MAAM,GAAG,MAAM,GAAG,IAAI,CAgB1D;AAED;;;;;;;GAOG;AACH,wBAAgB,YAAY,CAAC,GAAG,EAAE,MAAM,GAAG,MAAM,GAAG,IAAI,CAevD;AAED,MAAM,WAAW,qBAAqB;IACpC,qDAAqD;IACrD,YAAY,EAAE,MAAM,CAAC;IACrB,2EAA2E;IAC3E,SAAS,EAAE,MAAM,CAAC;CACnB;AAED;;;;;;;;;;GAUG;AACH,wBAAgB,2BAA2B,CACzC,SAAS,EAAE,MAAM,EACjB,SAAS,EAAE,MAAM,GAChB,qBAAqB,GAAG,IAAI,CA2B9B;AAED,gEAAgE;AAChE,wBAAgB,uBAAuB,CAAC,CAAC,EAAE,qBAAqB,GAAG,MAAM,CASxE;AAED;;;;GAIG;AACH,wBAAgB,sBAAsB,CAAC,CAAC,EAAE,qBAAqB,GAAG,MAAM,CAOvE"}

package/lib/dist/sync/worktree.js

@@ -52,6 +52,7 @@ var __importStar = (this && this.__importStar) || (function () {
 })();
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.gitWorktreeRoot = gitWorktreeRoot;
+exports.gitCommonDir = gitCommonDir;
 exports.detectWorktreeIndexMismatch = detectWorktreeIndexMismatch;
 exports.worktreeMismatchWarning = worktreeMismatchWarning;
 exports.worktreeMismatchNotice = worktreeMismatchNotice;
@@ -73,6 +74,10 @@ function gitWorktreeRoot(dir) {
             encoding: 'utf8',
             stdio: ['ignore', 'pipe', 'ignore'],
             windowsHide: true,
+            // Bounded like every git call in extraction/: this runs (memoized) on
+            // the daemon's main event loop, where an unbounded hang would trip the
+            // 60s liveness watchdog and SIGKILL a healthy daemon (#1139).
+            timeout: 5000,
         }).trim();
         return out ? realpath(out) : null;
     }
@@ -80,6 +85,32 @@ function gitWorktreeRoot(dir) {
         return null;
     }
 }
+/**
+ * Absolute, symlink-resolved git **common** directory for `dir` — the shared
+ * `.git` that all worktrees of one repository point at. Linked worktrees of the
+ * same repo report the SAME common dir; a submodule or an embedded clone is a
+ * DIFFERENT repository and reports its own (`…/.git/modules/<name>` or its own
+ * `.git`). That distinction is what separates a genuine "borrowed worktree"
+ * from a nested repo the parent index already covers. Null when not a repo.
+ */
+function gitCommonDir(dir) {
+    try {
+        const out = (0, child_process_1.execFileSync)('git', ['rev-parse', '--git-common-dir'], {
+            cwd: dir,
+            encoding: 'utf8',
+            stdio: ['ignore', 'pipe', 'ignore'],
+            windowsHide: true,
+            timeout: 5000, // same rationale as gitWorktreeRoot
+        }).trim();
+        if (!out)
+            return null;
+        // `--git-common-dir` is relative to cwd unless already absolute.
+        return realpath(path.isAbsolute(out) ? out : path.resolve(dir, out));
+    }
+    catch {
+        return null;
+    }
+}
 /**
  * Detect when `startPath` lives in one git working tree but the resolved
  * CodeGraph index (`indexRoot`) belongs to a *different* working tree.
@@ -103,6 +134,20 @@ function detectWorktreeIndexMismatch(startPath, indexRoot) {
     // plain ancestor directory", and avoids warning outside git entirely.
     if (gitWorktreeRoot(resolvedIndexRoot) !== resolvedIndexRoot)
         return null;
+    // Don't flag a nested repo (submodule / embedded clone) that `indexRoot`'s
+    // index ALREADY covers: indexing a super-repo descends into its submodules
+    // and gitlinked clones, so a query run from inside one resolves up to the
+    // parent index — whose graph *does* contain that nested repo's files. The
+    // warning's premise ("results are a different branch; symbols changed only
+    // here are missing") is false there, and its "run codegraph init -i" advice
+    // would needlessly fragment the unified workspace index. A genuine borrowed
+    // worktree and the index root are the SAME repository (they share a git
+    // common dir); a submodule/embedded clone is a DIFFERENT repository and does
+    // not — so suppress only when the two clearly differ. (#1031, #1033)
+    const worktreeCommon = gitCommonDir(worktreeRoot);
+    const indexCommon = gitCommonDir(resolvedIndexRoot);
+    if (worktreeCommon && indexCommon && worktreeCommon !== indexCommon)
+        return null;
     return { worktreeRoot, indexRoot: resolvedIndexRoot };
 }
 /** One-line-per-fact warning describing a detected mismatch. */

package/lib/dist/sync/worktree.js.map

@@ -1 +1 @@
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+{"version":3,"file":"worktree.js","sourceRoot":"","sources":["../../src/sync/worktree.ts"],"names":[],"mappings":";AAAA;;;;;;;;;;;;;;;;;GAiBG;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;AAcH,0CAgBC;AAUD,oCAeC;AAoBD,kEA8BC;AAGD,0DASC;AAOD,wDAOC;AAjID,uCAAyB;AACzB,2CAA6B;AAC7B,iDAA6C;AAE7C;;;;;;;GAOG;AACH,SAAgB,eAAe,CAAC,GAAW;IACzC,IAAI,CAAC;QACH,MAAM,GAAG,GAAG,IAAA,4BAAY,EAAC,KAAK,EAAE,CAAC,WAAW,EAAE,iBAAiB,CAAC,EAAE;YAChE,GAAG,EAAE,GAAG;YACR,QAAQ,EAAE,MAAM;YAChB,KAAK,EAAE,CAAC,QAAQ,EAAE,MAAM,EAAE,QAAQ,CAAC;YACnC,WAAW,EAAE,IAAI;YACjB,sEAAsE;YACtE,uEAAuE;YACvE,8DAA8D;YAC9D,OAAO,EAAE,IAAI;SACd,CAAC,CAAC,IAAI,EAAE,CAAC;QACV,OAAO,GAAG,CAAC,CAAC,CAAC,QAAQ,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC;IACpC,CAAC;IAAC,MAAM,CAAC;QACP,OAAO,IAAI,CAAC;IACd,CAAC;AACH,CAAC;AAED;;;;;;;GAOG;AACH,SAAgB,YAAY,CAAC,GAAW;IACtC,IAAI,CAAC;QACH,MAAM,GAAG,GAAG,IAAA,4BAAY,EAAC,KAAK,EAAE,CAAC,WAAW,EAAE,kBAAkB,CAAC,EAAE;YACjE,GAAG,EAAE,GAAG;YACR,QAAQ,EAAE,MAAM;YAChB,KAAK,EAAE,CAAC,QAAQ,EAAE,MAAM,EAAE,QAAQ,CAAC;YACnC,WAAW,EAAE,IAAI;YACjB,OAAO,EAAE,IAAI,EAAE,oCAAoC;SACpD,CAAC,CAAC,IAAI,EAAE,CAAC;QACV,IAAI,CAAC,GAAG;YAAE,OAAO,IAAI,CAAC;QACtB,iEAAiE;QACjE,OAAO,QAAQ,CAAC,IAAI,CAAC,UAAU,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,IAAI,CAAC,OAAO,CAAC,GAAG,EAAE,GAAG,CAAC,CAAC,CAAC;IACvE,CAAC;IAAC,MAAM,CAAC;QACP,OAAO,IAAI,CAAC;IACd,CAAC;AACH,CAAC;AASD;;;;;;;;;;GAUG;AACH,SAAgB,2BAA2B,CACzC,SAAiB,EACjB,SAAiB;IAEjB,MAAM,YAAY,GAAG,eAAe,CAAC,SAAS,CAAC,CAAC;IAChD,IAAI,CAAC,YAAY;QAAE,OAAO,IAAI,CAAC;IAE/B,MAAM,iBAAiB,GAAG,QAAQ,CAAC,SAAS,CAAC,CAAC;IAC9C,IAAI,YAAY,KAAK,iBAAiB;QAAE,OAAO,IAAI,CAAC;IAEpD,4EAA4E;IAC5E,0EAA0E;IAC1E,sEAAsE;IACtE,IAAI,eAAe,CAAC,iBAAiB,CAAC,KAAK,iBAAiB;QAAE,OAAO,IAAI,CAAC;IAE1E,2EAA2E;IAC3E,2EAA2E;IAC3E,0EAA0E;IAC1E,0EAA0E;IAC1E,2EAA2E;IAC3E,4EAA4E;IAC5E,4EAA4E;IAC5E,wEAAwE;IACxE,6EAA6E;IAC7E,qEAAqE;IACrE,MAAM,cAAc,GAAG,YAAY,CAAC,YAAY,CAAC,CAAC;IAClD,MAAM,WAAW,GAAG,YAAY,CAAC,iBAAiB,CAAC,CAAC;IACpD,IAAI,cAAc,IAAI,WAAW,IAAI,cAAc,KAAK,WAAW;QAAE,OAAO,IAAI,CAAC;IAEjF,OAAO,EAAE,YAAY,EAAE,SAAS,EAAE,iBAAiB,EAAE,CAAC;AACxD,CAAC;AAED,gEAAgE;AAChE,SAAgB,uBAAuB,CAAC,CAAwB;IAC9D,OAAO,CACL,iEAAiE;QACjE,iBAAiB,CAAC,CAAC,YAAY,IAAI;QACnC,iBAAiB,CAAC,CAAC,SAAS,IAAI;QAChC,mFAAmF;QACnF,kFAAkF;QAClF,6BAA6B,CAC9B,CAAC;AACJ,CAAC;AAED;;;;GAIG;AACH,SAAgB,sBAAsB,CAAC,CAAwB;IAC7D,OAAO,CACL,iEAAiE,CAAC,CAAC,SAAS,KAAK;QACjF,6BAA6B,CAAC,CAAC,YAAY,uCAAuC;QAClF,gFAAgF;QAChF,uBAAuB,CACxB,CAAC;AACJ,CAAC;AAED;;;;;;;;GAQG;AACH,SAAS,QAAQ,CAAC,CAAS;IACzB,IAAI,CAAC;QACH,OAAO,EAAE,CAAC,YAAY,CAAC,MAAM,CAAC,IAAI,CAAC,OAAO,CAAC,CAAC,CAAC,CAAC,CAAC;IACjD,CAAC;IAAC,MAAM,CAAC;QACP,OAAO,IAAI,CAAC,OAAO,CAAC,CAAC,CAAC,CAAC;IACzB,CAAC;AACH,CAAC"}

package/lib/dist/types.d.ts

@@ -20,7 +20,7 @@ export type EdgeKind = 'contains' | 'calls' | 'imports' | 'exports' | 'extends'
  * Supported programming languages. See NODE_KINDS for why this is a
  * runtime-iterable const array.
  */
-export declare const LANGUAGES: readonly ["typescript", "javascript", "tsx", "jsx", "python", "go", "rust", "java", "c", "cpp", "csharp", "razor", "php", "ruby", "swift", "kotlin", "dart", "svelte", "vue", "astro", "liquid", "pascal", "scala", "lua", "luau", "objc", "r", "vba", "sql", "yaml", "twig", "xml", "properties", "unknown"];
+export declare const LANGUAGES: readonly ["typescript", "javascript", "tsx", "jsx", "arkts", "python", "go", "rust", "java", "c", "cpp", "csharp", "razor", "php", "ruby", "swift", "kotlin", "dart", "svelte", "vue", "astro", "liquid", "pascal", "scala", "lua", "luau", "objc", "r", "vba", "sql", "solidity", "nix", "yaml", "twig", "xml", "properties", "cfml", "cfscript", "cfquery", "cobol", "vbnet", "erlang", "terraform", "unknown"];
 export type Language = (typeof LANGUAGES)[number];
 /**
  * A node in the knowledge graph representing a code symbol
@@ -261,11 +261,34 @@ export interface SearchOptions {
 export interface SearchResult {
     /** Matching node */
     node: Node;
-    /** Relevance score (0-1) */
+    /**
+     * Relevance score for relative ranking only — higher is more relevant.
+     * NOT normalized and NOT a 0-1 fraction: the FTS path returns an unbounded
+     * BM25 magnitude (often in the tens or hundreds), while the fuzzy/exact
+     * paths return ~0-1. Use it to order results, not as an absolute percentage.
+     */
     score: number;
     /** Matched text snippets for highlighting */
     highlights?: string[];
 }
+/**
+ * A symbol whose name-segments match prose words from a prompt — the
+ * graph-derived signal behind the front-load hook's medium tier
+ * (CodeGraph.getSegmentMatches). Always verified to exist in `nodes` at the
+ * time it is returned.
+ */
+export interface SegmentMatch {
+    /** Symbol name as indexed (e.g. `OrderStateMachine`). */
+    name: string;
+    /** Kind of the representative definition. */
+    kind: NodeKind;
+    /** File of the representative definition. */
+    filePath: string;
+    /** 1-based start line of the representative definition. */
+    startLine: number;
+    /** The prompt words (normalized) that matched this name's segments. */
+    matchedWords: string[];
+}
 /**
  * Context information for code understanding
  */

package/lib/dist/types.d.ts.map

@@ -1 +1 @@
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package/lib/dist/types.js

@@ -73,6 +73,7 @@ exports.LANGUAGES = [
     'javascript',
     'tsx',
     'jsx',
+    'arkts',
     'python',
     'go',
     'rust',
@@ -102,10 +103,19 @@ exports.LANGUAGES = [
     // `references` edges to the tables it names. Only treated as a query when a
     // sibling `queries.json` manifest is present (see directory discovery).
     'sql',
+    'solidity',
+    'nix',
     'yaml',
     'twig',
     'xml',
     'properties',
+    'cfml',
+    'cfscript',
+    'cfquery',
+    'cobol',
+    'vbnet',
+    'erlang',
+    'terraform',
     'unknown',
 ];
 //# sourceMappingURL=types.js.map

package/lib/dist/types.js.map

@@ -1 +1 @@
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package/lib/dist/upgrade/index.d.ts

@@ -23,9 +23,9 @@
  * process to exit (releasing the lock), then runs `install.ps1`. This is the
  * conventional Windows self-update dance (rustup/nvm-windows do the same).
  */
-export declare const REPO = "ardelperal/codegraph";
+export declare const REPO = "ardelperal/codegraph-vba";
 export declare const NPM_PACKAGE = "codegraph-vba";
-export declare const INSTALL_SH_URL = "https://raw.githubusercontent.com/ardelperal/codegraph/main/install.sh";
+export declare const INSTALL_SH_URL = "https://raw.githubusercontent.com/ardelperal/codegraph-vba/main/install.sh";
 export type InstallMethod = {
     kind: 'bundle';
     os: 'unix' | 'windows';
@@ -106,6 +106,11 @@ export interface UpgradeDeps {
     resolveLatest: (pin?: string) => Promise<string>;
     /** Run a command inheriting stdio; returns its exit code (-1 = spawn failed). */
     run: (cmd: string, args: string[], env?: NodeJS.ProcessEnv) => number;
+    /** Run a command capturing stdout (nothing reaches the terminal); null = spawn failed. */
+    capture: (cmd: string, args: string[]) => {
+        code: number;
+        stdout: string;
+    } | null;
     hasCommand: (cmd: string) => boolean;
     log: (msg: string) => void;
     warn: (msg: string) => void;
@@ -118,8 +123,30 @@ export declare function reindexAdvisory(): string;
  * Returns the process exit code (0 = success / nothing to do, 1 = failure).
  */
 export declare function runUpgrade(opts: UpgradeOptions, deps: UpgradeDeps): Promise<number>;
+type VersionProbe = 'match' | 'mismatch' | 'inconclusive';
+/**
+ * Prove the upgrade actually took: spawn the `codegraph` this terminal's PATH
+ * resolves and compare its reported version to the target. Catches the silent
+ * failure mode where ANOTHER install shadows the one we just upgraded (issue
+ * #1071 — e.g. a stale `npm i -g` copy earlier on PATH than the bundle
+ * launcher): the upgrade "succeeds" but `codegraph -v` — in this terminal and
+ * every future one — keeps serving the old version. Exported for unit tests.
+ */
+export declare function verifyResolvedVersion(latest: string, deps: UpgradeDeps): VersionProbe;
 /** Build the in-place Windows upgrade script (exported for unit-testing). */
 export declare function buildWindowsUpgradeScript(bundleRoot: string, version: string, arch: string): string;
+/**
+ * How to invoke npm. On Windows npm is a .cmd batch file, which Node refuses
+ * to spawn without a shell (EINVAL since the CVE-2024-27980 hardening) — a
+ * direct `npm.cmd` spawn fails on every current Node, so route it through
+ * cmd.exe, the same way the surface-refresh step invokes the .cmd launcher.
+ * (Verified live on the Windows VM: `spawnSync('npm.cmd')` → EINVAL;
+ * `cmd.exe /d /s /c npm …` → works.)
+ */
+export declare function npmInvocation(platform: NodeJS.Platform, npmArgs: string[]): {
+    cmd: string;
+    args: string[];
+};
 /**
  * True if `cmd` resolves to an executable on PATH. A pure-Node PATH scan — NOT
  * a spawned `command -v`/`which`: `command` is a shell builtin (no standalone
@@ -129,4 +156,9 @@ export declare function buildWindowsUpgradeScript(bundleRoot: string, version: s
  */
 export declare function hasCommand(cmd: string): boolean;
 export declare function defaultRun(cmd: string, args: string[], env?: NodeJS.ProcessEnv): number;
+export declare function defaultCapture(cmd: string, args: string[]): {
+    code: number;
+    stdout: string;
+} | null;
+export {};
 //# sourceMappingURL=index.d.ts.map

package/lib/dist/upgrade/index.d.ts.map

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package/lib/dist/upgrade/index.js

@@ -70,14 +70,17 @@ exports.parseLatestTagFromLocation = parseLatestTagFromLocation;
 exports.resolveLatestVersion = resolveLatestVersion;
 exports.reindexAdvisory = reindexAdvisory;
 exports.runUpgrade = runUpgrade;
+exports.verifyResolvedVersion = verifyResolvedVersion;
 exports.buildWindowsUpgradeScript = buildWindowsUpgradeScript;
+exports.npmInvocation = npmInvocation;
 exports.hasCommand = hasCommand;
 exports.defaultRun = defaultRun;
+exports.defaultCapture = defaultCapture;
 const fs = __importStar(require("fs"));
 const path = __importStar(require("path"));
 const https = __importStar(require("https"));
 const child_process_1 = require("child_process");
-exports.REPO = 'ardelperal/codegraph';
+exports.REPO = 'ardelperal/codegraph-vba';
 exports.NPM_PACKAGE = 'codegraph-vba';
 const RAW_BASE = `https://raw.githubusercontent.com/${exports.REPO}/main`;
 exports.INSTALL_SH_URL = `${RAW_BASE}/install.sh`;
@@ -119,17 +122,18 @@ function detectInstallMethod(input) {
     // (a Windows layout resolves correctly even when unit-tested on macOS/Linux).
     const P = isWin ? path.win32 : path.posix;
     const binDir = P.dirname(input.filename); // <…>/bin
-    // Bundle: <root>/lib/dist/bin/codegraph.js → <root> is up 3 from bin/.
-    // A bundle has a vendored node + a launcher script as siblings of lib/.
-    const bundleRoot = P.resolve(binDir, '..', '..', '..');
-    const vendoredNode = P.join(bundleRoot, isWin ? 'node.exe' : 'node');
-    const launcher = P.join(bundleRoot, 'bin', isWin ? 'codegraph.cmd' : 'codegraph');
-    if (exists(vendoredNode) && exists(launcher)) {
-        const os = isWin ? 'windows' : 'unix';
-        return { kind: 'bundle', os, bundleRoot, installDir: deriveInstallDir(bundleRoot, os, exists) };
-    }
     const norm = toPosix(input.filename);
+    // Path-based checks come FIRST. The npm thin-installer's per-platform
+    // package (@colbymchenry/codegraph-<platform>-<arch>) is itself a complete
+    // bundle — vendored node + bin/ launcher — living inside node_modules, so
+    // the layout sniff below would misread every npm install as a standalone
+    // bundle. `upgrade` would then curl install.sh into ~/.codegraph: a SECOND
+    // install that never wins the PATH race against npm's shim, leaving
+    // `codegraph -v` permanently on the old version (the #1071 shadow,
+    // self-inflicted). A path under node_modules is authoritative about HOW the
+    // user installed, whatever the artifact inside looks like.
     // npx cache: <…>/_npx/<hash>/node_modules/@colbymchenry/codegraph/…
+    // (checked before npm — the npx cache path also contains /node_modules/).
     if (norm.includes('/_npx/')) {
         return { kind: 'npx' };
     }
@@ -138,6 +142,15 @@ function detectInstallMethod(input) {
         const underCwd = norm.startsWith(toPosix(P.resolve(input.cwd)) + '/');
         return { kind: 'npm', scope: underCwd ? 'local' : 'global' };
     }
+    // Bundle: <root>/lib/dist/bin/codegraph.js → <root> is up 3 from bin/.
+    // A bundle has a vendored node + a launcher script as siblings of lib/.
+    const bundleRoot = P.resolve(binDir, '..', '..', '..');
+    const vendoredNode = P.join(bundleRoot, isWin ? 'node.exe' : 'node');
+    const launcher = P.join(bundleRoot, 'bin', isWin ? 'codegraph.cmd' : 'codegraph');
+    if (exists(vendoredNode) && exists(launcher)) {
+        const os = isWin ? 'windows' : 'unix';
+        return { kind: 'bundle', os, bundleRoot, installDir: deriveInstallDir(bundleRoot, os, exists) };
+    }
     // Source checkout: running <repo>/dist/bin/codegraph.js with a sibling .git.
     const repoRoot = P.resolve(binDir, '..', '..');
     if (exists(P.join(repoRoot, 'package.json')) && exists(P.join(repoRoot, '.git'))) {
@@ -406,15 +419,123 @@ async function runUpgrade(opts, deps) {
     // an existing Claude config, and skipped entirely by the kill-switch. Never
     // fatal to the upgrade.
     if (code === 0) {
+        let probe = 'inconclusive';
+        try {
+            probe = reportResolvedVersion(latest, deps);
+        }
+        catch {
+            /* an inconclusive probe must not fail the upgrade */
+        }
         try {
             await selfHealPromptHook(deps);
         }
         catch {
             /* a hook-wiring hiccup must not fail the upgrade */
         }
+        // The refresh executes whatever `codegraph` PATH resolves. If the probe
+        // just proved that's a stale shadowed install, spawning it would rewrite
+        // the agent surfaces with the very templates the refresh exists to heal —
+        // skip, and point at the manual command for after the PATH is fixed.
+        if (probe !== 'mismatch') {
+            try {
+                selfHealInstalledSurfaces(deps);
+            }
+            catch {
+                /* a refresh hiccup must not fail the upgrade */
+            }
+        }
+        else {
+            deps.log(c.dim('Skipped refreshing agent instructions/config — run `codegraph install --refresh` once the PATH is fixed.'));
+        }
     }
     return code;
 }
+/**
+ * Prove the upgrade actually took: spawn the `codegraph` this terminal's PATH
+ * resolves and compare its reported version to the target. Catches the silent
+ * failure mode where ANOTHER install shadows the one we just upgraded (issue
+ * #1071 — e.g. a stale `npm i -g` copy earlier on PATH than the bundle
+ * launcher): the upgrade "succeeds" but `codegraph -v` — in this terminal and
+ * every future one — keeps serving the old version. Exported for unit tests.
+ */
+function verifyResolvedVersion(latest, deps) {
+    if (!deps.hasCommand('codegraph'))
+        return 'inconclusive';
+    // Windows installs expose codegraph through a .cmd launcher; Node can't
+    // spawn .cmd files without a shell, so route through cmd.exe there.
+    const probe = deps.platform === 'win32'
+        ? deps.capture('cmd.exe', ['/d', '/s', '/c', 'codegraph --version'])
+        : deps.capture('codegraph', ['--version']);
+    if (!probe || probe.code !== 0)
+        return 'inconclusive';
+    // `codegraph --version` prints the bare version; take the last non-empty
+    // line so a stray runtime warning above it can't spoil the parse.
+    const reported = probe.stdout.trim().split(/\r?\n/).pop()?.trim() ?? '';
+    if (!parseSemver(reported))
+        return 'inconclusive';
+    return compareVersions(reported, latest) === 0 ? 'match' : 'mismatch';
+}
+/**
+ * Log the outcome of the post-upgrade version probe. On a match the user
+ * knows the current terminal is already serving the new version; on a
+ * mismatch they get told exactly which stale install is hijacking their PATH
+ * instead of discovering it via a mysteriously unchanged `codegraph -v`.
+ * Inconclusive probes fall back to the old soft hint — never a scare on
+ * setups we can't inspect (no `codegraph` on PATH yet, exotic wrappers).
+ * Returns the probe result so the caller can gate the post-upgrade refresh
+ * (which spawns the PATH-resolved binary) on it.
+ */
+function reportResolvedVersion(latest, deps) {
+    const { method } = deps;
+    // A project-local npm install isn't served by PATH's `codegraph` (that
+    // would be some other install) — a probe could only false-alarm.
+    if (method.kind === 'npm' && method.scope === 'local')
+        return 'inconclusive';
+    const probe = verifyResolvedVersion(latest, deps);
+    switch (probe) {
+        case 'match':
+            deps.log(c.green(`✓ \`codegraph\` on your PATH now reports ${latest} — this terminal is already using it.`));
+            break;
+        case 'mismatch':
+            deps.warn(`Installed ${latest}, but the \`codegraph\` this terminal resolves still reports an older version.`);
+            deps.log(c.dim('Another CodeGraph install earlier on your PATH is shadowing the one just upgraded.'));
+            deps.log(c.dim('Find every copy with `which -a codegraph` (Windows: `where codegraph`) and remove or upgrade the stale one.'));
+            break;
+        case 'inconclusive':
+            deps.log(c.dim('Open a new terminal if `codegraph --version` looks unchanged (PATH cache).'));
+            break;
+    }
+    return probe;
+}
+/**
+ * Refresh the agent surfaces previous installs wrote — the marker-fenced
+ * instructions sections (CLAUDE.md / AGENTS.md / GEMINI.md), MCP entries,
+ * legacy-hook cleanups — so they match the version that will serve them.
+ * Unlike the prompt hook above, this content is NOT version-agnostic: the
+ * templates are baked into the binary, so the still-running old process
+ * would only rewrite its own stale copy — the exact staleness this heals.
+ * We therefore spawn the freshly-installed binary (`codegraph install
+ * --refresh`), which is refresh-only: agents never configured stay
+ * untouched, and permission / prompt-hook choices are preserved. Gated on
+ * `codegraph` being resolvable on PATH (an npm-local install isn't) and on
+ * the kill-switch; never fatal to the upgrade.
+ */
+function selfHealInstalledSurfaces(deps) {
+    if (process.env.CODEGRAPH_NO_INSTALL_REFRESH === '1')
+        return;
+    if (!deps.hasCommand('codegraph'))
+        return;
+    deps.log(c.dim('Refreshing agent instruction sections and config written by previous versions…'));
+    // Windows installs expose codegraph through a .cmd launcher. Node cannot
+    // spawn .cmd files directly without a shell, so route the constant command
+    // through cmd.exe there (the same launcher a terminal would resolve).
+    const code = deps.platform === 'win32'
+        ? deps.run('cmd.exe', ['/d', '/s', '/c', 'codegraph install --refresh'])
+        : deps.run('codegraph', ['install', '--refresh']);
+    if (code !== 0) {
+        deps.warn('Could not refresh the installed agent surfaces — run `codegraph install --refresh` manually.');
+    }
+}
 /**
  * Wire the Claude `UserPromptSubmit` front-load hook on upgrade for an
  * already-configured global Claude install. No-op when Claude isn't configured,
@@ -454,7 +575,9 @@ function upgradeUnixBundle(method, pinned, deps) {
         return 1;
     }
     deps.log('');
-    deps.log(c.green('✓ Upgrade complete.') + c.dim(' Open a new terminal if the version looks unchanged (PATH cache).'));
+    // No "open a new terminal" hedge here — after the swap, runUpgrade probes
+    // the PATH-resolved `codegraph --version` and reports the real outcome.
+    deps.log(c.green('✓ Upgrade complete.'));
     deps.log(reindexAdvisory());
     return 0;
 }
@@ -507,17 +630,33 @@ function upgradeWindowsBundle(method, latest, deps) {
         return 1;
     }
     deps.log('');
-    deps.log(c.green('✓ Upgrade complete.') + c.dim(' Open a new terminal to be safe (PATH/version cache).'));
+    // The running node.exe was renamed aside, so the version probe in
+    // runUpgrade already exercises the NEW binary — no terminal hedge needed.
+    deps.log(c.green('✓ Upgrade complete.'));
     deps.log(reindexAdvisory());
     return 0;
 }
+/**
+ * How to invoke npm. On Windows npm is a .cmd batch file, which Node refuses
+ * to spawn without a shell (EINVAL since the CVE-2024-27980 hardening) — a
+ * direct `npm.cmd` spawn fails on every current Node, so route it through
+ * cmd.exe, the same way the surface-refresh step invokes the .cmd launcher.
+ * (Verified live on the Windows VM: `spawnSync('npm.cmd')` → EINVAL;
+ * `cmd.exe /d /s /c npm …` → works.)
+ */
+function npmInvocation(platform, npmArgs) {
+    if (platform === 'win32') {
+        return { cmd: 'cmd.exe', args: ['/d', '/s', '/c', ['npm', ...npmArgs].join(' ')] };
+    }
+    return { cmd: 'npm', args: npmArgs };
+}
 function upgradeNpm(method, versionSpec, deps) {
-    const npm = deps.platform === 'win32' ? 'npm.cmd' : 'npm';
     const args = method.scope === 'global'
         ? ['install', '-g', `${exports.NPM_PACKAGE}@${versionSpec}`]
         : ['install', `${exports.NPM_PACKAGE}@${versionSpec}`];
-    deps.log(c.dim(`Running: ${npm} ${args.join(' ')}`));
-    const code = deps.run(npm, args, process.env);
+    deps.log(c.dim(`Running: npm ${args.join(' ')}`));
+    const inv = npmInvocation(deps.platform, args);
+    const code = deps.run(inv.cmd, inv.args, process.env);
     if (code !== 0) {
         deps.error(`npm exited with code ${code}.`);
         if (method.scope === 'global') {
@@ -568,9 +707,19 @@ function defaultRun(cmd, args, env) {
         stdio: 'inherit',
         env: env ?? process.env,
         shell: process.platform === 'win32',
+        windowsHide: true,
     });
     if (r.error)
         return -1;
     return r.status ?? -1;
 }
+function defaultCapture(cmd, args) {
+    // stdio is piped (the default with `encoding`), so nothing the probed
+    // command prints reaches the user's terminal. The timeout keeps a wedged
+    // probe from hanging the upgrade's last step.
+    const r = (0, child_process_1.spawnSync)(cmd, args, { encoding: 'utf-8', windowsHide: true, timeout: 30_000 });
+    if (r.error)
+        return null;
+    return { code: r.status ?? -1, stdout: r.stdout ?? '' };
+}
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