@pella-labs/pinakes 0.1.0

package/dist/cli/index.js

@@ -0,0 +1,172 @@
+#!/usr/bin/env node
+import { auditCommand, renderAudit } from './audit.js';
+import { exportCommand, renderExport } from './export.js';
+import { importCommand, renderImport } from './import.js';
+import { purgeCommand, renderPurge } from './purge.js';
+import { rebuildCommand } from './rebuild.js';
+import { renderStatus, statusCommand } from './status.js';
+import { serveCommand } from './serve.js';
+import { logger } from '../observability/logger.js';
+function parseFlags(argv) {
+    const flags = {};
+    const positional = [];
+    for (let i = 0; i < argv.length; i++) {
+        const arg = argv[i];
+        if (arg.startsWith('--')) {
+            const eqIdx = arg.indexOf('=');
+            if (eqIdx > 0) {
+                flags[arg.slice(2, eqIdx)] = arg.slice(eqIdx + 1);
+            }
+            else {
+                const next = argv[i + 1];
+                if (next && !next.startsWith('--')) {
+                    flags[arg.slice(2)] = next;
+                    i++;
+                }
+                else {
+                    flags[arg.slice(2)] = true;
+                }
+            }
+        }
+        else {
+            positional.push(arg);
+        }
+    }
+    return { flags, positional };
+}
+function getString(flags, key) {
+    const v = flags[key];
+    return typeof v === 'string' ? v : undefined;
+}
+function getRequiredString(flags, key) {
+    const v = getString(flags, key);
+    if (!v)
+        throw new Error(`missing required flag: --${key}`);
+    return v;
+}
+async function main() {
+    const argv = process.argv.slice(2);
+    const subcommand = argv[0];
+    const { flags } = parseFlags(argv.slice(1));
+    switch (subcommand) {
+        case 'serve': {
+            await serveCommand({
+                wikiPath: getRequiredString(flags, 'wiki-path'),
+                dbPath: getString(flags, 'db-path'),
+                profilePath: getString(flags, 'profile-path'),
+                profileDbPath: getString(flags, 'profile-db-path'),
+            });
+            break;
+        }
+        case 'rebuild': {
+            const scope = getString(flags, 'scope');
+            const summaries = await rebuildCommand({
+                wikiPath: getRequiredString(flags, 'wiki-path'),
+                dbPath: getString(flags, 'db-path'),
+                profilePath: getString(flags, 'profile-path'),
+                profileDbPath: getString(flags, 'profile-db-path'),
+                scope,
+            });
+            for (const s of summaries) {
+                // eslint-disable-next-line no-console
+                console.log(`${s.scope.padEnd(8)} files=${s.files} nodes=${s.nodes} ` +
+                    `chunks_added=${s.chunks_added} chunks_skipped=${s.chunks_skipped} ` +
+                    `embedder_calls=${s.embedder_calls} duration=${s.durationMs}ms`);
+            }
+            break;
+        }
+        case 'status': {
+            const statuses = statusCommand({
+                dbPath: getString(flags, 'db-path'),
+                wikiPath: getString(flags, 'wiki-path'),
+                profileDbPath: getString(flags, 'profile-db-path'),
+            });
+            // eslint-disable-next-line no-console
+            console.log(renderStatus(statuses));
+            break;
+        }
+        case 'audit': {
+            const rows = auditCommand({
+                n: getString(flags, 'n') ? parseInt(getString(flags, 'n'), 10) : undefined,
+                dbPath: getString(flags, 'db-path'),
+                wikiPath: getString(flags, 'wiki-path'),
+                profileDbPath: getString(flags, 'profile-db-path'),
+                scope: getString(flags, 'scope') ?? undefined,
+            });
+            // eslint-disable-next-line no-console
+            console.log(renderAudit(rows));
+            break;
+        }
+        case 'purge': {
+            const scope = getRequiredString(flags, 'scope');
+            const result = purgeCommand({
+                scope,
+                confirm: flags['confirm'] === true,
+                dbPath: getString(flags, 'db-path'),
+                wikiPath: getString(flags, 'wiki-path'),
+                profileDbPath: getString(flags, 'profile-db-path'),
+            });
+            // eslint-disable-next-line no-console
+            console.log(renderPurge(result));
+            break;
+        }
+        case 'export': {
+            const scope = getRequiredString(flags, 'scope');
+            const out = getString(flags, 'out');
+            const data = exportCommand({
+                scope,
+                out,
+                dbPath: getString(flags, 'db-path'),
+                wikiPath: getString(flags, 'wiki-path'),
+                profileDbPath: getString(flags, 'profile-db-path'),
+            });
+            if (!out) {
+                // eslint-disable-next-line no-console
+                console.log(JSON.stringify(data, null, 2));
+            }
+            else {
+                // eslint-disable-next-line no-console
+                console.log(renderExport(data, out));
+            }
+            break;
+        }
+        case 'import': {
+            const scope = getRequiredString(flags, 'scope');
+            const result = importCommand({
+                scope,
+                inFile: getRequiredString(flags, 'in'),
+                dbPath: getString(flags, 'db-path'),
+                wikiPath: getString(flags, 'wiki-path'),
+                profileDbPath: getString(flags, 'profile-db-path'),
+            });
+            // eslint-disable-next-line no-console
+            console.log(renderImport(result));
+            break;
+        }
+        case undefined:
+        case 'help':
+        case '-h':
+        case '--help': {
+            // eslint-disable-next-line no-console
+            console.log(`kg — KG-MCP CLI
+
+Usage:
+  kg serve   --wiki-path <dir> [--db-path <path>] [--profile-path <dir>] [--profile-db-path <path>]
+  kg rebuild --wiki-path <dir> [--db-path <path>] [--scope project|personal|both]
+  kg status  [--db-path <path>] [--wiki-path <dir>] [--profile-db-path <path>]
+  kg audit   [--tail] [--n <count>] [--scope project|personal] [--db-path <path>]
+  kg purge   --scope <project|personal> --confirm [--db-path <path>]
+  kg export  --scope <project|personal> [--out file.json] [--db-path <path>]
+  kg import  --scope <project|personal> --in file.json [--db-path <path>]`);
+            break;
+        }
+        default:
+            throw new Error(`unknown subcommand: ${subcommand}`);
+    }
+}
+main().catch((err) => {
+    logger.error({ err }, 'kg cli failed');
+    console.error(err instanceof Error ? err.message : err);
+    process.exit(1);
+});
+//# sourceMappingURL=index.js.map

package/dist/cli/index.js.map

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package/dist/cli/purge.d.ts

@@ -0,0 +1,23 @@
+/**
+ * `kg purge --scope <s> [--confirm]` — delete a scope's SQLite DB file.
+ *
+ * This is the nuclear option: wipes the DB entirely. The user can rebuild
+ * from markdown afterwards (`kg rebuild`). Requires `--confirm` flag to
+ * prevent accidental deletion.
+ */
+export interface PurgeOptions {
+    scope: 'project' | 'personal';
+    confirm?: boolean;
+    dbPath?: string;
+    wikiPath?: string;
+    profileDbPath?: string;
+}
+export interface PurgeResult {
+    scope: string;
+    dbPath: string;
+    deleted: boolean;
+    reason?: string;
+}
+export declare function purgeCommand(options: PurgeOptions): PurgeResult;
+export declare function renderPurge(result: PurgeResult): string;
+//# sourceMappingURL=purge.d.ts.map

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

@@ -0,0 +1 @@
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package/dist/cli/purge.js

@@ -0,0 +1,57 @@
+import { existsSync, unlinkSync } from 'node:fs';
+import { homedir } from 'node:os';
+import { dirname, isAbsolute, resolve } from 'node:path';
+export function purgeCommand(options) {
+    const dbPath = resolveDbPath(options, options.scope);
+    if (!options.confirm) {
+        return {
+            scope: options.scope,
+            dbPath,
+            deleted: false,
+            reason: 'pass --confirm to actually delete the database',
+        };
+    }
+    if (!existsSync(dbPath)) {
+        return {
+            scope: options.scope,
+            dbPath,
+            deleted: false,
+            reason: 'database file does not exist',
+        };
+    }
+    // Remove the main DB file and WAL/SHM sidecars if present
+    unlinkSync(dbPath);
+    for (const suffix of ['-wal', '-shm']) {
+        const sidecar = dbPath + suffix;
+        if (existsSync(sidecar))
+            unlinkSync(sidecar);
+    }
+    return { scope: options.scope, dbPath, deleted: true };
+}
+export function renderPurge(result) {
+    if (result.deleted) {
+        return `purged ${result.scope} DB: ${result.dbPath}`;
+    }
+    return `${result.scope} DB NOT deleted: ${result.reason} (${result.dbPath})`;
+}
+// ----------------------------------------------------------------------------
+// Path helpers
+// ----------------------------------------------------------------------------
+function resolveDbPath(options, scope) {
+    if (scope === 'personal') {
+        if (options.profileDbPath)
+            return resolveAbs(options.profileDbPath);
+        const env = process.env.KG_PROFILE_PATH;
+        const profileDir = env ? resolveAbs(env) : resolve(homedir(), '.pharos/profile');
+        return resolve(profileDir, 'kg.db');
+    }
+    if (options.dbPath)
+        return resolveAbs(options.dbPath);
+    if (options.wikiPath)
+        return resolve(dirname(resolveAbs(options.wikiPath)), 'kg.db');
+    return resolve(process.cwd(), '.pharos/kg.db');
+}
+function resolveAbs(p) {
+    return isAbsolute(p) ? p : resolve(process.cwd(), p);
+}
+//# sourceMappingURL=purge.js.map

package/dist/cli/purge.js.map

@@ -0,0 +1 @@
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package/dist/cli/rebuild.d.ts

@@ -0,0 +1,54 @@
+import { type Embedder } from '../retrieval/embedder.js';
+/**
+ * `kg rebuild` — full-rebuild-from-markdown CLI subcommand for KG-MCP Phase 2.
+ *
+ * Walks the wiki directory, calls `IngesterService.ingestFile` for every
+ * markdown file, prints a summary. Default behavior: ingest both project and
+ * personal scope (if `--profile-path` resolves to a directory that exists).
+ * Pass `--scope project` or `--scope personal` to narrow.
+ *
+ * **Why "rebuild" and not "ingest"**: this is the markdown-canonical recovery
+ * path (CLAUDE.md §What this is — "If the index is corrupted or lost, rebuild
+ * it from the markdown source"). It's the answer to "my SQLite file got
+ * deleted / sqlite-vec broke / I changed the embedder model". The chokidar
+ * watcher in Pass 3 is the steady-state ingest path.
+ *
+ * **Performance budget**: <10s for the fixture (PRD acceptance criterion #5).
+ * On 100-file repos this should still complete in <2 minutes; the embedder
+ * is the bottleneck (~50ms per chunk × ~3 chunks per file = 150ms per file
+ * cold; warm chunks via per-chunk SHA skip drop this to ~5ms).
+ */
+export interface RebuildOptions {
+    /** Project wiki directory (required) */
+    wikiPath: string;
+    /** Project DB path (default: `<wikiPath>/../kg.db`) */
+    dbPath?: string;
+    /** Personal wiki directory (default: `~/.pharos/profile/wiki`) */
+    profilePath?: string;
+    /** Personal DB path (default: `<profilePath>/../kg.db`) */
+    profileDbPath?: string;
+    /** Which scopes to rebuild: 'project' | 'personal' | 'both' (default: 'both', falls back to 'project' if profile dir missing) */
+    scope?: 'project' | 'personal' | 'both';
+    /**
+     * Optional embedder injection — used by tests so they can pass a `CountingEmbedder`
+     * instead of loading the real model. Default: `TransformersEmbedder` singleton.
+     */
+    embedder?: Embedder;
+}
+export interface RebuildSummary {
+    scope: 'project' | 'personal';
+    files: number;
+    nodes: number;
+    chunks_added: number;
+    chunks_skipped: number;
+    embedder_calls: number;
+    durationMs: number;
+}
+/**
+ * Run a full-rebuild against one or both scopes. Returns a list of summaries
+ * (one per scope actually ingested). Throws on a fatal error per scope but
+ * continues to the next scope so a corrupted personal DB doesn't block the
+ * project rebuild (or vice versa).
+ */
+export declare function rebuildCommand(options: RebuildOptions): Promise<RebuildSummary[]>;
+//# sourceMappingURL=rebuild.d.ts.map

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

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package/dist/cli/rebuild.js

@@ -0,0 +1,113 @@
+import { existsSync } from 'node:fs';
+import { homedir } from 'node:os';
+import { dirname, isAbsolute, resolve } from 'node:path';
+import { closeDb, openDb } from '../db/client.js';
+import { IngesterService } from '../ingest/ingester.js';
+import { listMarkdownFiles } from '../ingest/manifest.js';
+import { logger } from '../observability/logger.js';
+import { TransformersEmbedder } from '../retrieval/embedder.js';
+/**
+ * Run a full-rebuild against one or both scopes. Returns a list of summaries
+ * (one per scope actually ingested). Throws on a fatal error per scope but
+ * continues to the next scope so a corrupted personal DB doesn't block the
+ * project rebuild (or vice versa).
+ */
+export async function rebuildCommand(options) {
+    const summaries = [];
+    const projectWiki = resolveAbs(options.wikiPath);
+    if (!existsSync(projectWiki)) {
+        throw new Error(`wiki path does not exist: ${projectWiki}`);
+    }
+    const projectDbPath = resolveAbs(options.dbPath ?? defaultDbPathFor(projectWiki));
+    const profileWiki = resolveAbs(options.profilePath ?? defaultProfileWikiPath());
+    const profileDbPath = resolveAbs(options.profileDbPath ?? defaultDbPathFor(profileWiki));
+    const scope = options.scope ?? 'both';
+    const includeProject = scope === 'project' || scope === 'both';
+    const includePersonal = (scope === 'personal' || scope === 'both') && existsSync(profileWiki);
+    // Lazily construct the shared embedder once for both scopes.
+    const embedder = options.embedder ?? new TransformersEmbedder();
+    await embedder.warmup();
+    if (includeProject) {
+        const summary = await rebuildOneScope({
+            scope: 'project',
+            wikiDir: projectWiki,
+            dbPath: projectDbPath,
+            embedder,
+        });
+        summaries.push(summary);
+    }
+    if (includePersonal) {
+        const summary = await rebuildOneScope({
+            scope: 'personal',
+            wikiDir: profileWiki,
+            dbPath: profileDbPath,
+            embedder,
+        });
+        summaries.push(summary);
+    }
+    return summaries;
+}
+async function rebuildOneScope(args) {
+    const { scope, wikiDir, dbPath, embedder } = args;
+    const t0 = Date.now();
+    const bundle = openDb(dbPath);
+    try {
+        const ingester = new IngesterService(bundle, embedder, scope, wikiDir);
+        const files = listMarkdownFiles(wikiDir);
+        let nodes = 0;
+        let chunksAdded = 0;
+        let chunksSkipped = 0;
+        let embedderCalls = 0;
+        for (const file of files) {
+            try {
+                const result = await ingester.ingestFile(file);
+                nodes += result.nodes_written;
+                chunksAdded += result.chunks_added;
+                chunksSkipped += result.chunks_skipped;
+                embedderCalls += result.embedder_calls;
+            }
+            catch (err) {
+                logger.error({ err, file, scope }, 'rebuild: failed to ingest file');
+                // Continue with the next file rather than aborting the entire rebuild —
+                // partial progress is better than total failure here.
+            }
+        }
+        return {
+            scope,
+            files: files.length,
+            nodes,
+            chunks_added: chunksAdded,
+            chunks_skipped: chunksSkipped,
+            embedder_calls: embedderCalls,
+            durationMs: Date.now() - t0,
+        };
+    }
+    finally {
+        closeDb(bundle);
+    }
+}
+// ----------------------------------------------------------------------------
+// Path defaults
+// ----------------------------------------------------------------------------
+function resolveAbs(p) {
+    return isAbsolute(p) ? p : resolve(process.cwd(), p);
+}
+/**
+ * Default DB path for a given wiki directory: `<wikiDir>/../kg.db`. Lives
+ * next to the wiki dir, inside the same `.pharos/` folder. Locked decision
+ * for Phase 2 (per AskUserQuestion 2026-04-08).
+ */
+function defaultDbPathFor(wikiDir) {
+    return resolve(dirname(wikiDir), 'kg.db');
+}
+/**
+ * Default personal wiki path. Honors `KG_PROFILE_PATH` env var, else
+ * `~/.pharos/profile/wiki`.
+ */
+function defaultProfileWikiPath() {
+    const env = process.env.KG_PROFILE_PATH;
+    if (env)
+        return resolve(env, 'wiki');
+    return resolve(homedir(), '.pharos/profile/wiki');
+}
+//# sourceMappingURL=rebuild.js.map

package/dist/cli/rebuild.js.map

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package/dist/cli/serve.d.ts

@@ -0,0 +1,49 @@
+#!/usr/bin/env node
+import { McpServer } from '@modelcontextprotocol/sdk/server/mcp.js';
+/**
+ * `kg serve` — stdio MCP server for KG-MCP Phase 2.
+ *
+ * Replaces Phase 1's `src/spike.ts` with the production wiring:
+ *   1. Open project + (optional) personal SQLite DBs (one writer + 2 readers each)
+ *   2. Warm the embedder singleton
+ *   3. Run startup consistency check against the manifest → re-ingest stale files
+ *   4. Start chokidar watchers for both scopes (with 2s debounce, drop-oldest)
+ *   5. Build the McpServer + register `kg_search` and `kg_execute`
+ *   6. Connect to StdioServerTransport and listen
+ *
+ * Graceful shutdown on SIGTERM/SIGINT closes the watchers, drains in-flight
+ * ingests, closes the DBs, and exits within 2 seconds.
+ *
+ * Per CLAUDE.md §Security #1: only the project repository binding is exposed
+ * to the tool handlers in Phase 2. Personal-scope tool reads stay gated
+ * behind the existing Phase 5 check in the tool handlers — even though the
+ * personal-scope DB is fully populated by the watcher, the LLM can't read
+ * from it until the 15-test privacy adversarial suite lands in Phase 5.
+ */
+export interface ServeOptions {
+    /** Project wiki directory (required) */
+    wikiPath: string;
+    /** Project DB path (default: `<wikiPath>/../kg.db`) */
+    dbPath?: string;
+    /** Personal wiki directory (default: `~/.pharos/profile/wiki` if it exists, else skip personal) */
+    profilePath?: string;
+    /** Personal DB path (default: `<profilePath>/../kg.db`) */
+    profileDbPath?: string;
+}
+interface ServerHandle {
+    server: McpServer;
+    shutdown: (signal: string) => Promise<void>;
+}
+/**
+ * Build (but don't start) the stdio server. Exposed as a function so future
+ * tests / in-process integrations can construct a server without going
+ * through the CLI argv path.
+ */
+export declare function buildServer(options: ServeOptions): Promise<ServerHandle>;
+/**
+ * The CLI entry point: build the server, connect stdio, install signal
+ * handlers, listen forever.
+ */
+export declare function serveCommand(options: ServeOptions): Promise<void>;
+export {};
+//# sourceMappingURL=serve.d.ts.map

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

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