@pella-labs/pinakes 0.3.4 → 0.3.6

package/dist/cli/serve.js

@@ -7,11 +7,15 @@ import { StdioServerTransport } from '@modelcontextprotocol/sdk/server/stdio.js'
 import { closeDb, openDb } from '../db/client.js';
 import { Repository } from '../db/repository.js';
 import { ChokidarWatcher } from '../ingest/chokidar.js';
+import { RepoMirrorWatcher } from '../ingest/repo-mirror.js';
+import { scanRepoMarkdownFiles } from '../init/scanner.js';
+import { copyMarkdownToWiki } from '../init/copy.js';
+import { ensurePinakesIgnoreFile, loadIgnorePatterns, cleanIgnoredFromWiki } from '../init/ignore.js';
 import { IngesterService } from '../ingest/ingester.js';
 import { checkConsistency, listMarkdownFiles } from '../ingest/manifest.js';
 import { executeToolConfig, makeExecuteHandler } from '../mcp/tools/execute.js';
 import { searchToolConfig, makeSearchHandler } from '../mcp/tools/search.js';
-import { resolveAbs, projectWikiPath as defaultProjectWikiPath, projectDbPath as defaultProjectDbPath, projectAuditJsonlPath, personalWikiPath as defaultPersonalWikiPath, personalDbPath as defaultPersonalDbPath, personalAuditJsonlPath, projectDataDir, pinakesRoot, } from '../paths.js';
+import { resolveAbs, projectWikiPath as defaultProjectWikiPath, projectDbPath as defaultProjectDbPath, projectAuditJsonlPath, personalWikiPath as defaultPersonalWikiPath, personalDbPath as defaultPersonalDbPath, personalAuditJsonlPath, projectDataDir, pinakesRoot, legacyProjectWikiPath, ensurePinakesGitignore, } from '../paths.js';
 import { writeAuditRow } from '../observability/audit.js';
 import { child, logger } from '../observability/logger.js';
 import { installSighupHandler, metrics } from '../observability/metrics.js';
@@ -24,10 +28,23 @@ import { QuickJSExecutor } from '../sandbox/executor.js';
  */
 export async function buildServer(options) {
     const projectRoot = resolveAbs(options.projectRoot ?? process.cwd());
-    const projectWiki = resolveAbs(options.wikiPath ?? defaultProjectWikiPath(projectRoot));
+    // Ensure .pinakes/.gitignore and .pinakesignore exist before any wiki operations
+    ensurePinakesGitignore(projectRoot);
+    ensurePinakesIgnoreFile(projectRoot);
+    // Migrate wiki from old centralized location to in-repo path
+    migrateLegacyWikiToInRepo(projectRoot);
+    const projectWiki = defaultProjectWikiPath(projectRoot);
     if (!existsSync(projectWiki)) {
+        // First run — seed wiki from all repo markdown files
+        const repoFiles = scanRepoMarkdownFiles(projectRoot);
         mkdirSync(projectWiki, { recursive: true });
-        logger.info({ path: projectWiki }, 'created wiki directory');
+        if (repoFiles.length > 0) {
+            const copyResult = copyMarkdownToWiki(repoFiles, projectRoot, projectWiki);
+            logger.info({ copied: copyResult.files_copied, skipped: copyResult.files_skipped, bytes: copyResult.total_bytes }, 'seeded wiki from repo markdown files');
+        }
+        else {
+            logger.info({ path: projectWiki }, 'created empty wiki directory (no .md files found in repo)');
+        }
     }
     const projectDb = resolveAbs(options.dbPath ?? defaultProjectDbPath(projectRoot));
     migrateLegacyInProject(projectRoot, projectDb);
@@ -70,6 +87,30 @@ export async function buildServer(options) {
     if (personalWatcher && personalIngester) {
         await personalWatcher.start(makeOnEvent(personalIngester));
     }
+    // Step 5b: repo mirror watcher — one-way sync from project root → wiki
+    const repoMirror = new RepoMirrorWatcher({
+        projectRoot,
+        wikiRoot: projectWiki,
+    });
+    await repoMirror.start();
+    // Step 5c: watch .pinakesignore for changes — clean wiki on update
+    const pinakesIgnorePath = resolve(projectRoot, '.pinakesignore');
+    let ignoreWatcher = null;
+    try {
+        const chokidarMod = await import('chokidar');
+        ignoreWatcher = chokidarMod.default.watch(pinakesIgnorePath, { ignoreInitial: true });
+        ignoreWatcher.on('change', () => {
+            logger.info('.pinakesignore changed — cleaning ignored files from wiki');
+            const patterns = loadIgnorePatterns(projectRoot);
+            const removed = cleanIgnoredFromWiki(projectRoot, projectWiki, patterns);
+            if (removed > 0) {
+                logger.info({ removed }, 'cleaned ignored files from wiki');
+            }
+        });
+    }
+    catch (err) {
+        logger.warn({ err }, 'failed to watch .pinakesignore');
+    }
     // Step 6: build the MCP server
     const repository = new Repository(projectBundle, personalBundle);
     const executor = new QuickJSExecutor();
@@ -97,7 +138,7 @@ export async function buildServer(options) {
         'Only fall back to Grep/Read/Glob after checking the knowledge base, or when you need ' +
         'to find exact symbols, read specific source files, or make code changes. ' +
         `Use \`${executeToolName}\` for advanced operations: graph traversal, gap detection, writing new knowledge.`;
-    const mcp = new McpServer({ name: serverName, version: '0.3.4' }, { capabilities: { tools: {} }, instructions });
+    const mcp = new McpServer({ name: serverName, version: '0.3.6' }, { capabilities: { tools: {} }, instructions });
     mcp.registerTool(searchToolName, searchToolConfig, instrumentHandler(searchToolName, makeSearchHandler({
         repository, embedder, bundle: projectBundle,
         personalBundle: personalBundle ?? undefined,
@@ -159,6 +200,9 @@ export async function buildServer(options) {
         logger.info({ signal }, 'pinakes shutting down');
         try {
             clearInterval(healthCheckTimer);
+            if (ignoreWatcher)
+                await ignoreWatcher.close();
+            await repoMirror.stop();
             await projectWatcher.stop();
             if (personalWatcher)
                 await personalWatcher.stop();
@@ -242,14 +286,39 @@ async function runStartupConsistency(ingester, wikiDir, scope, writer) {
         }
     }
 }
+/**
+ * Migrate wiki from the old centralized `~/.pinakes/projects/<mangled>/wiki/`
+ * to the new in-repo `<projectRoot>/.pinakes/wiki/` path.
+ *
+ * Uses cpSync (not renameSync) because old and new paths may be on different
+ * filesystems. Safe: if copy fails, old data remains untouched.
+ */
+function migrateLegacyWikiToInRepo(projectRoot) {
+    const oldWiki = legacyProjectWikiPath(projectRoot);
+    const newWiki = defaultProjectWikiPath(projectRoot);
+    if (existsSync(oldWiki) && !existsSync(newWiki)) {
+        try {
+            mkdirSync(dirname(newWiki), { recursive: true });
+            cpSync(oldWiki, newWiki, { recursive: true });
+            rmSync(oldWiki, { recursive: true, force: true });
+            logger.info({ from: oldWiki, to: newWiki }, 'migrated wiki from centralized to in-repo path');
+        }
+        catch (err) {
+            logger.warn({ err, from: oldWiki, to: newWiki }, 'wiki migration failed — continuing');
+        }
+    }
+    else if (existsSync(oldWiki) && existsSync(newWiki)) {
+        logger.warn({ old: oldWiki, new: newWiki }, 'wiki exists at both legacy and in-repo paths — using in-repo path. Remove legacy path manually if no longer needed.');
+    }
+}
 /**
  * Migrate legacy data from in-project `.pinakes/` (or `kg.db`) to the new
  * centralized `~/.pinakes/projects/<mangled>/` layout.
  *
  * Handles three legacy layouts:
  *   1. `<projectRoot>/kg.db` — Phase 1 flat layout
- *   2. `<projectRoot>/.pinakes/` — Phase 2 in-project layout
- *   3. `~/.pharos/profile/` — legacy personal wiki location
+ *   2. `<projectRoot>/.pinakes/` — Phase 2 in-project layout (DB/manifest/audit only; wiki stays in-repo)
+ *   3. Orphaned manifest files in project root
  */
 function migrateLegacyInProject(projectRoot, newDbPath) {
     const targetDir = projectDataDir(projectRoot);
@@ -265,25 +334,26 @@ function migrateLegacyInProject(projectRoot, newDbPath) {
         }
         logger.info({ from: legacyDb, to: newDbPath }, 'migrated legacy kg.db');
     }
-    // 2. Legacy in-project .pinakes/ directory
+    // 2. Legacy in-project .pinakes/ — only migrate non-wiki items (DB, manifest,
+    //    audit) to centralized location. Wiki stays in-repo.
     const legacyPinakesDir = resolve(projectRoot, '.pinakes');
     if (existsSync(legacyPinakesDir) && legacyPinakesDir !== targetDir) {
         mkdirSync(targetDir, { recursive: true });
-        // Copy contents (DB, audit.jsonl, manifest.json, wiki/) to new location
-        // Only migrate files that don't already exist at the target
         try {
             const entries = readdirSync(legacyPinakesDir, { withFileTypes: true });
             for (const entry of entries) {
+                // Skip wiki/ and .gitignore — they belong in-repo
+                if (entry.name === 'wiki' || entry.name === '.gitignore')
+                    continue;
                 const src = resolve(legacyPinakesDir, entry.name);
                 const dst = resolve(targetDir, entry.name);
                 if (!existsSync(dst)) {
                     cpSync(src, dst, { recursive: true });
                     logger.info({ from: src, to: dst }, 'migrated legacy .pinakes entry');
                 }
+                // Remove the migrated source entry (but keep .pinakes/ dir since wiki lives there now)
+                rmSync(src, { recursive: true, force: true });
             }
-            // Remove old .pinakes/ after successful migration
-            rmSync(legacyPinakesDir, { recursive: true, force: true });
-            logger.info({ path: legacyPinakesDir }, 'removed legacy .pinakes/ directory');
         }
         catch (err) {
             logger.warn({ err, from: legacyPinakesDir, to: targetDir }, 'legacy .pinakes/ migration failed — continuing');

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package/dist/cli/status.d.ts

@@ -12,8 +12,6 @@ export interface StatusOptions {
     projectRoot?: string;
     /** Path to project DB override */
     dbPath?: string;
-    /** Path to project wiki dir (unused in new layout, kept for backwards compat) */
-    wikiPath?: string;
     /** Path to personal DB (default: `~/.pinakes/pinakes.db`) */
     profileDbPath?: string;
 }

package/dist/cli/status.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"status.d.ts","sourceRoot":"","sources":["../../src/cli/status.ts"],"names":[],"mappings":"AAMA;;;;;;;;GAQG;AAEH,MAAM,WAAW,aAAa;IAC5B,4CAA4C;IAC5C,WAAW,CAAC,EAAE,MAAM,CAAC;IACrB,kCAAkC;IAClC,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,6DAA6D;IAC7D,aAAa,CAAC,EAAE,MAAM,CAAC;CACxB;AAED,MAAM,WAAW,WAAW;IAC1B,KAAK,EAAE,SAAS,GAAG,UAAU,CAAC;IAC9B,MAAM,EAAE,MAAM,CAAC;IACf,MAAM,EAAE,OAAO,CAAC;IAChB,aAAa,EAAE,MAAM,GAAG,IAAI,CAAC;IAC7B,eAAe,EAAE,MAAM,GAAG,IAAI,CAAC;IAC/B,aAAa,EAAE,MAAM,GAAG,IAAI,CAAC;IAC7B,SAAS,EAAE,MAAM,CAAC,MAAM,EAAE,MAAM,CAAC,CAAC;CACnC;AAED;;;;GAIG;AACH,wBAAgB,aAAa,CAAC,OAAO,GAAE,aAAkB,GAAG,WAAW,EAAE,CAQxE;AAED;;;;GAIG;AACH,wBAAgB,YAAY,CAAC,QAAQ,EAAE,WAAW,EAAE,GAAG,MAAM,CAqB5D"}

package/dist/cli/status.js.map

@@ -1 +1 @@
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package/dist/ingest/repo-mirror.d.ts

@@ -0,0 +1,17 @@
+export interface RepoMirrorOptions {
+    projectRoot: string;
+    wikiRoot: string;
+}
+export declare class RepoMirrorWatcher {
+    private watcher;
+    private pending;
+    private readonly projectRoot;
+    private readonly wikiRoot;
+    private readonly ignorePatterns;
+    constructor(opts: RepoMirrorOptions);
+    start(): Promise<void>;
+    stop(): Promise<void>;
+    private queueMirror;
+    private executeMirror;
+}
+//# sourceMappingURL=repo-mirror.d.ts.map

package/dist/ingest/repo-mirror.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"repo-mirror.d.ts","sourceRoot":"","sources":["../../src/ingest/repo-mirror.ts"],"names":[],"mappings":"AAsBA,MAAM,WAAW,iBAAiB;IAChC,WAAW,EAAE,MAAM,CAAC;IACpB,QAAQ,EAAE,MAAM,CAAC;CAClB;AAQD,qBAAa,iBAAiB;IAC5B,OAAO,CAAC,OAAO,CAA0B;IACzC,OAAO,CAAC,OAAO,CAAyC;IACxD,OAAO,CAAC,QAAQ,CAAC,WAAW,CAAS;IACrC,OAAO,CAAC,QAAQ,CAAC,QAAQ,CAAS;IAClC,OAAO,CAAC,QAAQ,CAAC,cAAc,CAAkB;gBAErC,IAAI,EAAE,iBAAiB;IAM7B,KAAK,IAAI,OAAO,CAAC,IAAI,CAAC;IAgDtB,IAAI,IAAI,OAAO,CAAC,IAAI,CAAC;IAY3B,OAAO,CAAC,WAAW;IAoBnB,OAAO,CAAC,aAAa;CAmBtB"}

package/dist/ingest/repo-mirror.js

@@ -0,0 +1,124 @@
+import { cpSync, existsSync, mkdirSync, rmSync } from 'node:fs';
+import { dirname, relative, resolve } from 'node:path';
+import chokidar from 'chokidar';
+import { loadIgnorePatterns, shouldIgnore } from '../init/ignore.js';
+import { logger } from '../observability/logger.js';
+/**
+ * `RepoMirrorWatcher` — one-way sync from project repo → wiki directory.
+ *
+ * Watches `<projectRoot>` for `.md` file changes outside `.pinakes/wiki/`,
+ * and mirrors them into the wiki. The existing wiki `ChokidarWatcher` then
+ * picks up the copied file and indexes it.
+ *
+ * Direction: repo → wiki only. Wiki-only files (no repo counterpart) are
+ * never touched. Edits to mirrored files in the wiki will be overwritten
+ * on the next repo-side change.
+ */
+const DEBOUNCE_MS = 2_000;
+export class RepoMirrorWatcher {
+    watcher = null;
+    pending = new Map();
+    projectRoot;
+    wikiRoot;
+    ignorePatterns;
+    constructor(opts) {
+        this.projectRoot = resolve(opts.projectRoot);
+        this.wikiRoot = resolve(opts.wikiRoot);
+        this.ignorePatterns = loadIgnorePatterns(this.projectRoot);
+    }
+    async start() {
+        if (this.watcher)
+            throw new Error('RepoMirrorWatcher.start called twice');
+        this.watcher = chokidar.watch(this.projectRoot, {
+            ignoreInitial: true, // Don't mirror on startup — auto-seed already handled that
+            awaitWriteFinish: false,
+            ignored: [
+                '**/node_modules/**',
+                '**/.git/**',
+                '**/.pinakes/**',
+                '**/dist/**',
+                '**/build/**',
+                '**/coverage/**',
+                '**/.next/**',
+                '**/.nuxt/**',
+                '**/vendor/**',
+                '**/__pycache__/**',
+                '**/.tox/**',
+                '**/target/**',
+            ],
+        });
+        const shouldMirror = (path) => {
+            if (!path.toLowerCase().endsWith('.md'))
+                return false;
+            const rel = relative(this.projectRoot, resolve(path));
+            return !shouldIgnore(rel, this.ignorePatterns);
+        };
+        this.watcher.on('add', (path) => {
+            if (shouldMirror(path))
+                this.queueMirror('copy', path);
+        });
+        this.watcher.on('change', (path) => {
+            if (shouldMirror(path))
+                this.queueMirror('copy', path);
+        });
+        this.watcher.on('unlink', (path) => {
+            if (shouldMirror(path))
+                this.queueMirror('remove', path);
+        });
+        this.watcher.on('error', (err) => {
+            logger.error({ err }, 'repo mirror watcher error');
+        });
+        await new Promise((resolveWait) => {
+            this.watcher.once('ready', () => resolveWait());
+        });
+        logger.info({ projectRoot: this.projectRoot }, 'repo mirror watcher started');
+    }
+    async stop() {
+        for (const pending of this.pending.values()) {
+            clearTimeout(pending.timer);
+        }
+        this.pending.clear();
+        if (this.watcher) {
+            await this.watcher.close();
+            this.watcher = null;
+        }
+    }
+    queueMirror(kind, sourcePath) {
+        const abs = resolve(sourcePath);
+        const existing = this.pending.get(abs);
+        if (existing) {
+            existing.kind = kind;
+            existing.sourcePath = abs;
+            return;
+        }
+        const timer = setTimeout(() => {
+            const pending = this.pending.get(abs);
+            this.pending.delete(abs);
+            if (pending) {
+                this.executeMirror(pending);
+            }
+        }, DEBOUNCE_MS);
+        this.pending.set(abs, { kind, sourcePath: abs, timer });
+    }
+    executeMirror(pending) {
+        const rel = relative(this.projectRoot, pending.sourcePath);
+        if (rel.startsWith('..'))
+            return; // safety
+        const target = resolve(this.wikiRoot, rel);
+        try {
+            if (pending.kind === 'copy') {
+                mkdirSync(dirname(target), { recursive: true });
+                cpSync(pending.sourcePath, target);
+                logger.debug({ source: pending.sourcePath, target }, 'repo mirror: copied');
+            }
+            else if (pending.kind === 'remove' && existsSync(target)) {
+                rmSync(target);
+                logger.debug({ target }, 'repo mirror: removed');
+            }
+        }
+        catch (err) {
+            logger.warn({ err, source: pending.sourcePath, target }, 'repo mirror: operation failed');
+        }
+    }
+}
+//# sourceMappingURL=repo-mirror.js.map

package/dist/ingest/repo-mirror.js.map

@@ -0,0 +1 @@
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package/dist/init/copy.d.ts

@@ -0,0 +1,18 @@
+export interface CopyResult {
+    files_copied: number;
+    files_skipped: number;
+    total_bytes: number;
+}
+/**
+ * Copy markdown files from the project repo into the wiki directory,
+ * preserving relative directory structure.
+ *
+ * Idempotent: skips files that already exist in the target. This allows
+ * re-running `pinakes init` without overwriting curated wiki edits.
+ *
+ * @param files Absolute paths to source markdown files
+ * @param projectRoot Absolute path to the project root
+ * @param wikiRoot Absolute path to the wiki directory (`<project>/.pinakes/wiki/`)
+ */
+export declare function copyMarkdownToWiki(files: string[], projectRoot: string, wikiRoot: string): CopyResult;
+//# sourceMappingURL=copy.d.ts.map

package/dist/init/copy.d.ts.map

@@ -0,0 +1 @@
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package/dist/init/copy.js

@@ -0,0 +1,40 @@
+import { cpSync, existsSync, mkdirSync, statSync } from 'node:fs';
+import { dirname, relative, resolve } from 'node:path';
+import { logger } from '../observability/logger.js';
+/**
+ * Copy markdown files from the project repo into the wiki directory,
+ * preserving relative directory structure.
+ *
+ * Idempotent: skips files that already exist in the target. This allows
+ * re-running `pinakes init` without overwriting curated wiki edits.
+ *
+ * @param files Absolute paths to source markdown files
+ * @param projectRoot Absolute path to the project root
+ * @param wikiRoot Absolute path to the wiki directory (`<project>/.pinakes/wiki/`)
+ */
+export function copyMarkdownToWiki(files, projectRoot, wikiRoot) {
+    const result = { files_copied: 0, files_skipped: 0, total_bytes: 0 };
+    for (const absPath of files) {
+        const rel = relative(projectRoot, absPath);
+        // Safety: skip files that resolve outside the project root
+        if (rel.startsWith('..'))
+            continue;
+        const target = resolve(wikiRoot, rel);
+        if (existsSync(target)) {
+            result.files_skipped++;
+            continue;
+        }
+        try {
+            mkdirSync(dirname(target), { recursive: true });
+            cpSync(absPath, target);
+            const size = statSync(target).size;
+            result.total_bytes += size;
+            result.files_copied++;
+        }
+        catch (err) {
+            logger.warn({ err, source: absPath, target }, 'failed to copy file to wiki');
+        }
+    }
+    return result;
+}
+//# sourceMappingURL=copy.js.map

package/dist/init/copy.js.map

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package/dist/init/ignore.d.ts

@@ -0,0 +1,29 @@
+export interface IgnorePattern {
+    /** The original pattern string (for debugging) */
+    raw: string;
+    /** Whether this is a negation pattern (starts with !) */
+    negate: boolean;
+    /** The test function */
+    test: (relativePath: string) => boolean;
+}
+/**
+ * Load ignore patterns from `.pinakesignore` in the project root,
+ * merged with built-in defaults. User patterns override defaults.
+ */
+export declare function loadIgnorePatterns(projectRoot: string): IgnorePattern[];
+/**
+ * Create a default `.pinakesignore` in the project root if one doesn't exist.
+ * Called during serve startup alongside .gitignore generation.
+ */
+export declare function ensurePinakesIgnoreFile(projectRoot: string): void;
+/**
+ * Remove wiki files that match the current ignore patterns.
+ * Called when `.pinakesignore` changes to clean up previously-copied files.
+ */
+export declare function cleanIgnoredFromWiki(_projectRoot: string, wikiRoot: string, patterns: IgnorePattern[]): number;
+/**
+ * Check if a relative path should be ignored based on the patterns.
+ * Later patterns (including negations) override earlier ones.
+ */
+export declare function shouldIgnore(relativePath: string, patterns: IgnorePattern[]): boolean;
+//# sourceMappingURL=ignore.d.ts.map

package/dist/init/ignore.d.ts.map

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