@graphpilot-oss/graphpilot 0.0.1 → 0.1.0

package/dist/repo-resolve.d.ts

@@ -0,0 +1,47 @@
+/**
+ * Default repo-path resolution for MCP tool calls.
+ *
+ * Agents often omit `path` or pass "." while the MCP process cwd is the
+ * user's home directory — not the open workspace. Resolution order:
+ *
+ *   1. Explicit `path` argument
+ *   2. GRAPHPILOT_ROOT environment variable
+ *   3. MCP client workspace roots (roots/list)
+ *   4. Walk parents of process.cwd() for an on-disk index
+ *   5. Unique index whose rootPath contains cwd
+ *   6. Sole index under ~/.graphpilot
+ *   7. process.cwd() (may error with a helpful message)
+ */
+import { type Graph } from './storage.js';
+export interface IndexedRepoSummary {
+    rootPath: string;
+    repoId: string;
+    indexedAt: string;
+    symbolCount: number;
+    edgeCount: number;
+}
+export declare function setMcpClientRoots(roots: string[]): void;
+export declare function getMcpClientRoots(): readonly string[];
+/**
+ * Convert an MCP root URI to an absolute filesystem path.
+ * Supports file:// URIs (the common case from Cursor and VS Code).
+ */
+export declare function rootUriToFilesystemPath(uri: string): string | null;
+/** True when `child` is `parent` or a subdirectory of `parent`. */
+export declare function isPathUnder(child: string, parent: string): boolean;
+/**
+ * List every valid index under ~/.graphpilot by reading each graph.json.
+ * Best-effort: skips corrupt entries.
+ */
+export declare function listIndexedRepos(): IndexedRepoSummary[];
+/**
+ * Resolve which filesystem path to use for an MCP tool call before
+ * worktree re-rooting and graph loading.
+ */
+export declare function resolveRepoPath(rawPath?: string): string;
+/**
+ * Build a helpful error when no graph exists for the resolved root.
+ */
+export declare function formatNoIndexError(requestedPath: string, resolvedWorktreeRoot: string): string;
+/** @internal Test hook: summarize a loaded graph. */
+export declare function graphSummary(g: Graph): IndexedRepoSummary;

package/dist/repo-resolve.js

@@ -0,0 +1,195 @@
+/**
+ * Default repo-path resolution for MCP tool calls.
+ *
+ * Agents often omit `path` or pass "." while the MCP process cwd is the
+ * user's home directory — not the open workspace. Resolution order:
+ *
+ *   1. Explicit `path` argument
+ *   2. GRAPHPILOT_ROOT environment variable
+ *   3. MCP client workspace roots (roots/list)
+ *   4. Walk parents of process.cwd() for an on-disk index
+ *   5. Unique index whose rootPath contains cwd
+ *   6. Sole index under ~/.graphpilot
+ *   7. process.cwd() (may error with a helpful message)
+ */
+import { existsSync, readdirSync, readFileSync } from 'node:fs';
+import { homedir } from 'node:os';
+import { dirname, join, resolve } from 'node:path';
+import { fileURLToPath } from 'node:url';
+import { loadGraph } from './storage.js';
+import { resolveIndexRoot } from './git.js';
+/** Workspace roots reported by the MCP client via roots/list. */
+let mcpClientRoots = [];
+export function setMcpClientRoots(roots) {
+    mcpClientRoots = roots;
+}
+export function getMcpClientRoots() {
+    return mcpClientRoots;
+}
+/**
+ * Convert an MCP root URI to an absolute filesystem path.
+ * Supports file:// URIs (the common case from Cursor and VS Code).
+ */
+export function rootUriToFilesystemPath(uri) {
+    const trimmed = uri.trim();
+    if (!trimmed)
+        return null;
+    if (trimmed.startsWith('file://')) {
+        try {
+            return resolve(fileURLToPath(trimmed));
+        }
+        catch {
+            return null;
+        }
+    }
+    // Some clients may pass a plain path; accept only absolute-looking paths.
+    if (/^([A-Za-z]:[\\/]|\/)/.test(trimmed)) {
+        return resolve(trimmed);
+    }
+    return null;
+}
+function normalizeForCompare(p) {
+    return resolve(p).replace(/\\/g, '/').toLowerCase();
+}
+/** True when `child` is `parent` or a subdirectory of `parent`. */
+export function isPathUnder(child, parent) {
+    const c = normalizeForCompare(child);
+    const p = normalizeForCompare(parent);
+    return c === p || c.startsWith(p + '/');
+}
+/**
+ * List every valid index under ~/.graphpilot by reading each graph.json.
+ * Best-effort: skips corrupt entries.
+ */
+export function listIndexedRepos() {
+    const base = join(homedir(), '.graphpilot');
+    if (!existsSync(base))
+        return [];
+    const out = [];
+    let entries;
+    try {
+        entries = readdirSync(base);
+    }
+    catch {
+        return [];
+    }
+    for (const repoId of entries) {
+        const graphFile = join(base, repoId, 'graph.json');
+        if (!existsSync(graphFile))
+            continue;
+        let raw;
+        try {
+            raw = readFileSync(graphFile, 'utf8');
+        }
+        catch {
+            continue;
+        }
+        let parsed;
+        try {
+            parsed = JSON.parse(raw);
+        }
+        catch {
+            continue;
+        }
+        if (!parsed || typeof parsed !== 'object')
+            continue;
+        const o = parsed;
+        const rootPath = typeof o.rootPath === 'string' ? o.rootPath : null;
+        if (!rootPath)
+            continue;
+        const graph = loadGraph(rootPath);
+        if (!graph)
+            continue;
+        out.push({
+            rootPath: graph.rootPath,
+            repoId: graph.repoId,
+            indexedAt: graph.indexedAt,
+            symbolCount: graph.symbolCount,
+            edgeCount: graph.edgeCount,
+        });
+    }
+    return out.sort((a, b) => b.indexedAt.localeCompare(a.indexedAt));
+}
+function firstRootWithIndex(paths) {
+    for (const p of paths) {
+        const { root } = resolveIndexRoot(p);
+        if (loadGraph(root))
+            return p;
+    }
+    return null;
+}
+/**
+ * Resolve which filesystem path to use for an MCP tool call before
+ * worktree re-rooting and graph loading.
+ */
+export function resolveRepoPath(rawPath) {
+    if (rawPath !== undefined && rawPath.trim() !== '') {
+        return resolve(rawPath.trim());
+    }
+    const envRoot = process.env.GRAPHPILOT_ROOT?.trim();
+    if (envRoot) {
+        return resolve(envRoot);
+    }
+    const fromMcp = firstRootWithIndex([...mcpClientRoots]);
+    if (fromMcp)
+        return fromMcp;
+    let cur = resolve(process.cwd());
+    for (let i = 0; i < 64; i++) {
+        const { root } = resolveIndexRoot(cur);
+        if (loadGraph(root))
+            return cur;
+        const parent = dirname(cur);
+        if (parent === cur)
+            break;
+        cur = parent;
+    }
+    const indexed = listIndexedRepos();
+    const cwd = resolve(process.cwd());
+    const underCwd = indexed.filter((r) => isPathUnder(cwd, r.rootPath));
+    if (underCwd.length === 1) {
+        return resolve(underCwd[0].rootPath);
+    }
+    if (indexed.length === 1) {
+        return resolve(indexed[0].rootPath);
+    }
+    return cwd;
+}
+/**
+ * Build a helpful error when no graph exists for the resolved root.
+ */
+export function formatNoIndexError(requestedPath, resolvedWorktreeRoot) {
+    const indexed = listIndexedRepos();
+    const lines = [
+        `No GraphPilot index found for ${resolvedWorktreeRoot}.`,
+        `(Resolved from: ${requestedPath})`,
+        '',
+        'Fix:',
+        `  • Run \`graphpilot index ${resolvedWorktreeRoot}\` in a terminal, or`,
+        '  • Call the gp_index tool with the same path, or',
+        '  • Set GRAPHPILOT_ROOT to your workspace folder in MCP config, or',
+        '  • Use a Cursor/VS Code MCP client that supports workspace roots.',
+    ];
+    if (indexed.length > 0) {
+        lines.push('', 'Indexed repos on this machine:');
+        const cap = 8;
+        for (const r of indexed.slice(0, cap)) {
+            lines.push(`  • ${r.rootPath}  (${r.symbolCount} symbols, ${r.edgeCount} calls, ${r.indexedAt})`);
+        }
+        if (indexed.length > cap) {
+            lines.push(`  … and ${indexed.length - cap} more`);
+        }
+        lines.push('', 'Pass an explicit `path` to target one of the above.');
+    }
+    return lines.join('\n');
+}
+/** @internal Test hook: summarize a loaded graph. */
+export function graphSummary(g) {
+    return {
+        rootPath: g.rootPath,
+        repoId: g.repoId,
+        indexedAt: g.indexedAt,
+        symbolCount: g.symbolCount,
+        edgeCount: g.edgeCount,
+    };
+}
+//# sourceMappingURL=repo-resolve.js.map

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package/dist/storage.js

@@ -30,7 +30,8 @@ export function saveGraph(graph) {
     // fail T4's schema validator and force a full re-index. Defends watch
     // mode (which writes many times) against ungraceful shutdowns.
     const tmpPath = path + '.tmp';
-    writeFileSync(tmpPath, JSON.stringify(graph, null, 2), {
+    const pretty = process.env['GRAPHPILOT_PRETTY'] === '1';
+    writeFileSync(tmpPath, pretty ? JSON.stringify(graph, null, 2) : JSON.stringify(graph), {
         encoding: 'utf8',
         mode: 0o600,
     });
@@ -80,6 +81,14 @@ export function loadGraph(absRootPath) {
             '\n');
         return null;
     }
+    // Reject graphs whose stored rootPath doesn't match the directory we
+    // derived the storage path from. Guards against a graph.json copied from
+    // another project landing in a sibling repo's ~/.graphpilot/<id>/ slot.
+    if (validated.rootPath !== absRootPath) {
+        process.stderr.write(`[graphpilot] graph.json rootPath mismatch: stored "${validated.rootPath}" ` +
+            `but requested "${absRootPath}" — ignoring stale index.\n`);
+        return null;
+    }
     return validated;
 }
 //# sourceMappingURL=storage.js.map

package/dist/storage.js.map

@@ -1 +1 @@
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+{"version":3,"file":"storage.js","sourceRoot":"","sources":["../src/storage.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,UAAU,EAAE,MAAM,aAAa,CAAC;AACzC,OAAO,EAAE,OAAO,EAAE,MAAM,SAAS,CAAC;AAClC,OAAO,EAAE,IAAI,EAAE,MAAM,WAAW,CAAC;AACjC,OAAO,EAAE,SAAS,EAAE,aAAa,EAAE,YAAY,EAAE,UAAU,EAAE,SAAS,EAAE,UAAU,EAAE,MAAM,SAAS,CAAC;AAGpG,OAAO,EAAE,aAAa,EAAE,MAAM,mBAAmB,CAAC;AAElD,MAAM,SAAS,GAAG,OAAO,CAAC,QAAQ,KAAK,OAAO,CAAC;AAwB/C,MAAM,UAAU,SAAS,CAAC,WAAmB;IAC3C,OAAO,UAAU,CAAC,QAAQ,CAAC,CAAC,MAAM,CAAC,WAAW,CAAC,CAAC,MAAM,CAAC,KAAK,CAAC,CAAC,KAAK,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC;AAC7E,CAAC;AAED,MAAM,UAAU,OAAO,CAAC,WAAmB;IACzC,OAAO,IAAI,CAAC,OAAO,EAAE,EAAE,aAAa,EAAE,SAAS,CAAC,WAAW,CAAC,CAAC,CAAC;AAChE,CAAC;AAED,MAAM,UAAU,SAAS,CAAC,WAAmB;IAC3C,OAAO,IAAI,CAAC,OAAO,CAAC,WAAW,CAAC,EAAE,YAAY,CAAC,CAAC;AAClD,CAAC;AAED,MAAM,UAAU,SAAS,CAAC,KAAY;IACpC,MAAM,GAAG,GAAG,OAAO,CAAC,KAAK,CAAC,QAAQ,CAAC,CAAC;IACpC,2EAA2E;IAC3E,wEAAwE;IACxE,wEAAwE;IACxE,4EAA4E;IAC5E,yEAAyE;IACzE,4CAA4C;IAC5C,SAAS,CAAC,GAAG,EAAE,EAAE,SAAS,EAAE,IAAI,EAAE,IAAI,EAAE,KAAK,EAAE,CAAC,CAAC;IACjD,IAAI,CAAC,SAAS;QAAE,SAAS,CAAC,GAAG,EAAE,KAAK,CAAC,CAAC;IACtC,MAAM,IAAI,GAAG,SAAS,CAAC,KAAK,CAAC,QAAQ,CAAC,CAAC;IAEvC,sEAAsE;IACtE,uEAAuE;IACvE,sEAAsE;IACtE,+DAA+D;IAC/D,MAAM,OAAO,GAAG,IAAI,GAAG,MAAM,CAAC;IAC9B,MAAM,MAAM,GAAG,OAAO,CAAC,GAAG,CAAC,mBAAmB,CAAC,KAAK,GAAG,CAAC;IACxD,aAAa,CAAC,OAAO,EAAE,MAAM,CAAC,CAAC,CAAC,IAAI,CAAC,SAAS,CAAC,KAAK,EAAE,IAAI,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,SAAS,CAAC,KAAK,CAAC,EAAE;QACtF,QAAQ,EAAE,MAAM;QAChB,IAAI,EAAE,KAAK;KACZ,CAAC,CAAC;IACH,IAAI,CAAC,SAAS;QAAE,SAAS,CAAC,OAAO,EAAE,KAAK,CAAC,CAAC;IAC1C,UAAU,CAAC,OAAO,EAAE,IAAI,CAAC,CAAC;IAC1B,OAAO,IAAI,CAAC;AACd,CAAC;AAED;;;;;;;;;;;;;GAaG;AACH,MAAM,UAAU,SAAS,CAAC,WAAmB;IAC3C,MAAM,IAAI,GAAG,SAAS,CAAC,WAAW,CAAC,CAAC;IACpC,IAAI,CAAC,UAAU,CAAC,IAAI,CAAC;QAAE,OAAO,IAAI,CAAC;IAEnC,IAAI,GAAW,CAAC;IAChB,IAAI,CAAC;QACH,GAAG,GAAG,YAAY,CAAC,IAAI,EAAE,MAAM,CAAC,CAAC;IACnC,CAAC;IAAC,MAAM,CAAC;QACP,OAAO,IAAI,CAAC;IACd,CAAC;IAED,IAAI,MAAe,CAAC;IACpB,IAAI,CAAC;QACH,MAAM,GAAG,IAAI,CAAC,KAAK,CAAC,GAAG,CAAC,CAAC;IAC3B,CAAC;IAAC,MAAM,CAAC;QACP,OAAO,CAAC,MAAM,CAAC,KAAK,CAAC,8CAA8C,IAAI,IAAI,CAAC,CAAC;QAC7E,OAAO,IAAI,CAAC;IACd,CAAC;IAED,MAAM,MAAM,GAAa,EAAE,CAAC;IAC5B,MAAM,SAAS,GAAG,aAAa,CAAC,MAAM,EAAE,MAAM,CAAC,CAAC;IAChD,IAAI,CAAC,SAAS,EAAE,CAAC;QACf,OAAO,CAAC,MAAM,CAAC,KAAK,CAClB,qDAAqD,IAAI,IAAI;YAC3D,MAAM,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,OAAO,CAAC,EAAE,CAAC,CAAC,IAAI,CAAC,IAAI,CAAC;YACxC,IAAI,CACP,CAAC;QACF,OAAO,IAAI,CAAC;IACd,CAAC;IACD,qEAAqE;IACrE,yEAAyE;IACzE,wEAAwE;IACxE,IAAI,SAAS,CAAC,QAAQ,KAAK,WAAW,EAAE,CAAC;QACvC,OAAO,CAAC,MAAM,CAAC,KAAK,CAClB,sDAAsD,SAAS,CAAC,QAAQ,IAAI;YAC1E,kBAAkB,WAAW,6BAA6B,CAC7D,CAAC;QACF,OAAO,IAAI,CAAC;IACd,CAAC;IACD,OAAO,SAAS,CAAC;AACnB,CAAC"}

package/dist/validation.js

@@ -15,27 +15,44 @@ export const MAX_FILES_PER_INDEX = 50_000;
 const DANGEROUS_PATHS = new Set([
     '/',
     '/bin',
+    '/boot',
+    '/dev',
+    '/etc',
+    '/home',
+    '/lib',
+    '/lib64',
+    '/opt',
+    '/proc',
+    '/root',
+    '/run',
     '/sbin',
+    '/srv',
+    '/sys',
+    '/tmp',
     '/usr',
     '/usr/bin',
     '/usr/local',
-    '/etc',
     '/var',
-    '/tmp',
+    // macOS canonical forms (symlinks resolve to /private/*)
     '/private',
     '/private/etc',
     '/private/var',
     '/private/tmp',
+    // macOS top-level
+    '/Applications',
     '/Library',
     '/System',
-    '/Applications',
     '/Volumes',
     '/Users',
-    '/home',
+    // Windows system paths
     'C:\\Windows',
     'C:\\Windows\\System32',
     'C:\\Program Files',
     'C:\\Program Files (x86)',
+    // Indexing C:\Users walks every user profile on the machine; C:\ProgramData
+    // holds service configs and app state that should never be leaked.
+    'C:\\Users',
+    'C:\\ProgramData',
 ]);
 /**
  * Returns null if the path is safe to index, or a human-readable reason string
@@ -43,6 +60,13 @@ const DANGEROUS_PATHS = new Set([
  */
 export function validateRootPath(rawPath) {
     const abs = resolve(rawPath);
+    // Check the unnormalized absolute path first so that entries like /sbin are
+    // caught even on distros where /sbin is a symlink to /usr/sbin (merged-/usr
+    // layout on Debian/Ubuntu 22+ and Fedora). realpathSync would resolve it to
+    // /usr/sbin which is not in the set, causing a bypass.
+    if (DANGEROUS_PATHS.has(abs)) {
+        return `Refusing to index system path: ${abs}`;
+    }
     let real;
     try {
         real = realpathSync(abs);
@@ -54,6 +78,8 @@ export function validateRootPath(rawPath) {
     if (process.platform === 'win32' && /^[A-Za-z]:\\?$/.test(real)) {
         return `Refusing to index system path: ${real}`;
     }
+    // Also check the resolved form — catches cases where a non-dangerous-looking
+    // path resolves to a dangerous one via a symlink.
     if (DANGEROUS_PATHS.has(real)) {
         return `Refusing to index system path: ${real}`;
     }

package/dist/validation.js.map

@@ -1 +1 @@
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+{"version":3,"file":"validation.js","sourceRoot":"","sources":["../src/validation.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,YAAY,EAAE,MAAM,SAAS,CAAC;AACvC,OAAO,EAAE,OAAO,EAAE,MAAM,SAAS,CAAC;AAClC,OAAO,EAAE,OAAO,EAAE,MAAM,WAAW,CAAC;AAEpC,0EAA0E;AAC1E,MAAM,CAAC,MAAM,cAAc,GAAG,CAAC,GAAG,IAAI,GAAG,IAAI,CAAC,CAAC,OAAO;AAEtD,0EAA0E;AAC1E,MAAM,CAAC,MAAM,mBAAmB,GAAG,MAAM,CAAC;AAE1C;;;;;;GAMG;AACH,MAAM,eAAe,GAAG,IAAI,GAAG,CAAC;IAC9B,GAAG;IACH,MAAM;IACN,OAAO;IACP,MAAM;IACN,MAAM;IACN,OAAO;IACP,MAAM;IACN,QAAQ;IACR,MAAM;IACN,OAAO;IACP,OAAO;IACP,MAAM;IACN,OAAO;IACP,MAAM;IACN,MAAM;IACN,MAAM;IACN,MAAM;IACN,UAAU;IACV,YAAY;IACZ,MAAM;IACN,yDAAyD;IACzD,UAAU;IACV,cAAc;IACd,cAAc;IACd,cAAc;IACd,kBAAkB;IAClB,eAAe;IACf,UAAU;IACV,SAAS;IACT,UAAU;IACV,QAAQ;IACR,uBAAuB;IACvB,aAAa;IACb,uBAAuB;IACvB,mBAAmB;IACnB,yBAAyB;IACzB,4EAA4E;IAC5E,mEAAmE;IACnE,WAAW;IACX,iBAAiB;CAClB,CAAC,CAAC;AAEH;;;GAGG;AACH,MAAM,UAAU,gBAAgB,CAAC,OAAe;IAC9C,MAAM,GAAG,GAAG,OAAO,CAAC,OAAO,CAAC,CAAC;IAE7B,4EAA4E;IAC5E,4EAA4E;IAC5E,4EAA4E;IAC5E,uDAAuD;IACvD,IAAI,eAAe,CAAC,GAAG,CAAC,GAAG,CAAC,EAAE,CAAC;QAC7B,OAAO,kCAAkC,GAAG,EAAE,CAAC;IACjD,CAAC;IAED,IAAI,IAAY,CAAC;IACjB,IAAI,CAAC;QACH,IAAI,GAAG,YAAY,CAAC,GAAG,CAAC,CAAC;IAC3B,CAAC;IAAC,MAAM,CAAC;QACP,OAAO,6CAA6C,GAAG,EAAE,CAAC;IAC5D,CAAC;IAED,qEAAqE;IACrE,IAAI,OAAO,CAAC,QAAQ,KAAK,OAAO,IAAI,gBAAgB,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC;QAChE,OAAO,kCAAkC,IAAI,EAAE,CAAC;IAClD,CAAC;IACD,6EAA6E;IAC7E,kDAAkD;IAClD,IAAI,eAAe,CAAC,GAAG,CAAC,IAAI,CAAC,EAAE,CAAC;QAC9B,OAAO,kCAAkC,IAAI,EAAE,CAAC;IAClD,CAAC;IACD,IAAI,IAAI,KAAK,OAAO,EAAE,EAAE,CAAC;QACvB,OAAO,mDAAmD,IAAI,kDAAkD,CAAC;IACnH,CAAC;IACD,OAAO,IAAI,CAAC;AACd,CAAC"}

package/dist/watcher.d.ts

@@ -48,6 +48,9 @@ export declare class GraphWatcher {
     private watcher;
     private readonly log;
     private readonly awaitStabilityMs;
+    /** mtime + size of graph.json after the last save this process performed. */
+    private lastSavedMtimeMs;
+    private lastSavedSizeBytes;
     /**
      * Serializes the update queue so chokidar bursts (multiple `change`
      * events in 200ms) don't race each other into a torn graph.
@@ -75,6 +78,13 @@ export declare class GraphWatcher {
     private enqueue;
     private handleEvent;
     private handleDeletion;
+    /**
+     * If graph.json was written by another process since we last saved, reload
+     * it into memory so the next delta is applied on top of the fresh state.
+     * This handles gp_index from an agent, a parallel CLI re-index, or a
+     * git checkout while watch is running.
+     */
+    private reloadIfDrifted;
     /**
      * Apply a new (symbols, rawCalls) state: re-resolve edges, update the
      * graph object, save atomically.

package/dist/watcher.js

@@ -16,12 +16,12 @@
  * clean for any agent that's also reading the graph over MCP.
  */
 import chokidar from 'chokidar';
-import { realpathSync } from 'node:fs';
-import { resolve, relative } from 'node:path';
+import { realpathSync, statSync } from 'node:fs';
+import { resolve, relative, sep } from 'node:path';
 import { parseFile } from './parser.js';
 import { extractSymbols } from './symbols.js';
 import { extractRawCalls, resolveCallEdges } from './edges.js';
-import { saveGraph, loadGraph, repoIdFor } from './storage.js';
+import { saveGraph, loadGraph, repoIdFor, graphPath } from './storage.js';
 import { readGitInfo } from './git.js';
 import { indexDirectory } from './indexer.js';
 import { validateRootPath, MAX_FILES_PER_INDEX } from './validation.js';
@@ -63,6 +63,9 @@ export class GraphWatcher {
     watcher = null;
     log;
     awaitStabilityMs;
+    /** mtime + size of graph.json after the last save this process performed. */
+    lastSavedMtimeMs = 0;
+    lastSavedSizeBytes = 0;
     /**
      * Serializes the update queue so chokidar bursts (multiple `change`
      * events in 200ms) don't race each other into a torn graph.
@@ -84,6 +87,14 @@ export class GraphWatcher {
         if (loaded) {
             this.graph = loaded;
             this.rawCalls = this.deriveRawCalls(loaded.edges);
+            try {
+                const st = statSync(graphPath(this.absRoot));
+                this.lastSavedMtimeMs = st.mtimeMs;
+                this.lastSavedSizeBytes = st.size;
+            }
+            catch {
+                // best-effort baseline
+            }
         }
         else {
             // No existing index — caller is expected to `start()`, which will
@@ -142,10 +153,15 @@ export class GraphWatcher {
     async applyUpdate(absFilePath, kind = 'change') {
         if (!isWatchableFile(absFilePath))
             return null;
-        if (!absFilePath.startsWith(this.absRoot))
+        if (absFilePath !== this.absRoot && !absFilePath.startsWith(this.absRoot + sep))
             return null;
+        // Detect mtime drift — reload before computing the delta so we apply
+        // the edit on top of the freshest known graph, not a stale in-memory one.
+        this.reloadIfDrifted();
         const start = Date.now();
-        const rel = relative(this.absRoot, absFilePath);
+        // Normalize to POSIX separators so paths stored in graph.json are always
+        // forward-slash on every OS (same convention as indexer.ts).
+        const rel = relative(this.absRoot, absFilePath).split(sep).join('/');
         const symbolsBefore = this.graph.symbols.length;
         const edgesBefore = this.graph.edges.length;
         // 1. Remove existing symbols + raw calls from this file
@@ -186,10 +202,11 @@ export class GraphWatcher {
     }
     /** Drop everything that came from a deleted file. */
     async applyDeletion(absFilePath) {
-        if (!absFilePath.startsWith(this.absRoot))
+        if (absFilePath !== this.absRoot && !absFilePath.startsWith(this.absRoot + sep))
             return null;
+        this.reloadIfDrifted();
         const start = Date.now();
-        const rel = relative(this.absRoot, absFilePath);
+        const rel = relative(this.absRoot, absFilePath).split(sep).join('/');
         const symbolsBefore = this.graph.symbols.length;
         const edgesBefore = this.graph.edges.length;
         const keptSymbols = this.graph.symbols.filter((s) => s.file !== rel);
@@ -226,6 +243,14 @@ export class GraphWatcher {
         };
         this.rawCalls = this.deriveRawCalls(result.edges);
         saveGraph(this.graph);
+        try {
+            const st = statSync(graphPath(this.absRoot));
+            this.lastSavedMtimeMs = st.mtimeMs;
+            this.lastSavedSizeBytes = st.size;
+        }
+        catch {
+            // best-effort
+        }
     }
     /** Read-only accessor, mainly for tests + diagnostics. */
     get currentGraph() {
@@ -251,6 +276,36 @@ export class GraphWatcher {
     async handleDeletion(abs) {
         await this.applyDeletion(abs);
     }
+    /**
+     * If graph.json was written by another process since we last saved, reload
+     * it into memory so the next delta is applied on top of the fresh state.
+     * This handles gp_index from an agent, a parallel CLI re-index, or a
+     * git checkout while watch is running.
+     */
+    reloadIfDrifted() {
+        if (this.lastSavedMtimeMs === 0)
+            return; // no baseline yet
+        try {
+            const st = statSync(graphPath(this.absRoot));
+            // Check both mtime and size: mtime alone has 1-second resolution on some
+            // Windows filesystems (FAT/exFAT, some container mounts), so a rapid
+            // external write within the same second would not be detected. Adding the
+            // size check catches content changes even when the clock doesn't advance.
+            if (st.mtimeMs === this.lastSavedMtimeMs && st.size === this.lastSavedSizeBytes)
+                return;
+            const fresh = loadGraph(this.absRoot);
+            if (fresh) {
+                this.graph = fresh;
+                this.rawCalls = this.deriveRawCalls(fresh.edges);
+                this.lastSavedMtimeMs = st.mtimeMs;
+                this.lastSavedSizeBytes = st.size;
+                this.log(`Detected external re-index (${fresh.symbolCount} symbols); reloaded before applying delta.`);
+            }
+        }
+        catch {
+            // best-effort — if statSync fails the file is gone; next save will recreate it
+        }
+    }
     /**
      * Apply a new (symbols, rawCalls) state: re-resolve edges, update the
      * graph object, save atomically.
@@ -278,6 +333,14 @@ export class GraphWatcher {
         };
         this.rawCalls = rawCalls;
         saveGraph(this.graph);
+        try {
+            const st = statSync(graphPath(this.absRoot));
+            this.lastSavedMtimeMs = st.mtimeMs;
+            this.lastSavedSizeBytes = st.size;
+        }
+        catch {
+            // best-effort
+        }
     }
     finalize(file, kind, symbolsBefore, edgesBefore, start) {
         return {

package/dist/watcher.js.map

@@ -1 +1 @@
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