npm - @pella-labs/pinakes - Versions diffs - 0.6.1 → 0.6.2 - Mend

@pella-labs/pinakes 0.6.1 → 0.6.2

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Files changed (26) hide show

package/dist/cli/audit-wiki.d.ts.map +1 -1
package/dist/cli/audit-wiki.js +2 -2
package/dist/cli/audit-wiki.js.map +1 -1
package/dist/cli/contradiction-cli.d.ts.map +1 -1
package/dist/cli/contradiction-cli.js +2 -2
package/dist/cli/contradiction-cli.js.map +1 -1
package/dist/cli/crystallize.d.ts.map +1 -1
package/dist/cli/crystallize.js +2 -2
package/dist/cli/crystallize.js.map +1 -1
package/dist/cli/index.js +22 -2
package/dist/cli/index.js.map +1 -1
package/dist/cli/rebuild.d.ts.map +1 -1
package/dist/cli/rebuild.js +2 -2
package/dist/cli/rebuild.js.map +1 -1
package/dist/cli/serve.d.ts.map +1 -1
package/dist/cli/serve.js +16 -3
package/dist/cli/serve.js.map +1 -1
package/dist/init/reconcile.d.ts +26 -0
package/dist/init/reconcile.d.ts.map +1 -0
package/dist/init/reconcile.js +139 -0
package/dist/init/reconcile.js.map +1 -0
package/dist/paths.d.ts +15 -0
package/dist/paths.d.ts.map +1 -1
package/dist/paths.js +31 -2
package/dist/paths.js.map +1 -1
package/package.json +1 -1

package/dist/cli/audit-wiki.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
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1	+ {"version":3,"file":"audit-wiki.d.ts","sourceRoot":"","sources":["../../src/cli/audit-wiki.ts"],"names":[],"mappings":"AAGA,OAAO,KAAK,EAAE,QAAQ,IAAI,oBAAoB,EAAE,MAAM,gBAAgB,CAAC;AAGvE,OAAO,EAAa,KAAK,MAAM,EAAE,MAAM,qBAAqB,CAAC;AAC7D,OAAO,EAAqB,KAAK,WAAW,EAAE,MAAM,oBAAoB,CAAC;AAUzE,OAAO,EAAqB,KAAK,mBAAmB,EAAE,MAAM,oBAAoB,CAAC;AACjF,OAAO,EAAE,sBAAsB,EAAE,MAAM,eAAe,CAAC;AAgBvD,MAAM,WAAW,gBAAgB;IAC/B,WAAW,CAAC,EAAE,MAAM,CAAC;IACrB,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,KAAK,CAAC,EAAE,SAAS,GAAG,UAAU,CAAC;IAC/B,KAAK,CAAC,EAAE,OAAO,CAAC;IAChB,aAAa,CAAC,EAAE,OAAO,CAAC;CACzB;AAED,MAAM,WAAW,eAAe;IAC9B,cAAc,EAAE,mBAAmB,CAAC;IACpC,UAAU,EAAE,MAAM,CAAC;IACnB,aAAa,EAAE,MAAM,CAAC;IACtB,eAAe,EAAE,MAAM,CAAC;IACxB,iBAAiB,EAAE,MAAM,CAAC;IAC1B,iBAAiB,EAAE,MAAM,CAAC;CAC3B;AAED,wBAAsB,gBAAgB,CAAC,IAAI,EAAE,gBAAgB,GAAG,OAAO,CAAC,eAAe,CAAC,CAgHvF;AAkBD,wBAAsB,aAAa,CACjC,IAAI,EAAE,MAAM,EAAE,EACd,WAAW,EAAE,WAAW,EACxB,QAAQ,CAAC,EAAE;IAAE,IAAI,EAAE,CAAC,KAAK,EAAE,MAAM,EAAE,MAAM,CAAC,EAAE,MAAM,KAAK,IAAI,CAAA;CAAE,GAC5D,OAAO,CAAC,MAAM,EAAE,CAAC,CAgCnB;AAED,wBAAgB,sBAAsB,CAAC,QAAQ,EAAE,MAAM,GAAG,MAAM,EAAE,CAYjE;AAMD,MAAM,WAAW,WAAW;IAC1B,KAAK,EAAE,MAAM,CAAC;IACd,SAAS,EAAE,MAAM,CAAC;IAClB,MAAM,EAAE,gBAAgB,CAAC;CAC1B;AAED,wBAAgB,gBAAgB,CAC9B,MAAM,EAAE,oBAAoB,EAC5B,KAAK,EAAE,MAAM,GACZ,WAAW,EAAE,CA0Bf;AAMD,MAAM,WAAW,UAAU;IACzB,KAAK,EAAE,MAAM,CAAC;IACd,QAAQ,EAAE,KAAK,CAAC;QAAE,UAAU,EAAE,MAAM,CAAC;QAAC,OAAO,EAAE,MAAM,CAAA;KAAE,CAAC,CAAC;CAC1D;AAED,wBAAgB,iBAAiB,CAC/B,MAAM,EAAE,oBAAoB,EAC5B,KAAK,EAAE,MAAM,EACb,IAAI,EAAE,MAAM,EAAE,GACb,UAAU,EAAE,CA4Bd;AAeD,wBAAsB,sBAAsB,CAC1C,IAAI,EAAE,MAAM,EAAE,EACd,QAAQ,EAAE,UAAU,EAAE,EACtB,QAAQ,EAAE,MAAM,EAChB,WAAW,EAAE,WAAW,EACxB,QAAQ,CAAC,EAAE,UAAU,CAAC,OAAO,sBAAsB,CAAC,GACnD,OAAO,CAAC,MAAM,CAAC,CAkDjB;AAMD,MAAM,WAAW,aAAa;IAC5B,UAAU,EAAE,MAAM,CAAC;IACnB,WAAW,EAAE,MAAM,CAAC;IACpB,UAAU,EAAE,MAAM,CAAC;IACnB,UAAU,EAAE,MAAM,CAAC;CACpB;AAED,wBAAgB,gBAAgB,CAC9B,MAAM,EAAE,oBAAoB,EAC5B,KAAK,EAAE,MAAM,GACZ,aAAa,CAoBf;AAqID;;;;;;;;;GASG;AACH,wBAAgB,SAAS,CAAC,KAAK,EAAE,MAAM,GAAG,OAAO,CAgChD"}

package/dist/cli/audit-wiki.js CHANGED Viewed

@@ -3,7 +3,7 @@ import { join } from 'node:path';
 import { closeDb, openDb } from '../db/client.js';
 import { queryGaps } from '../gaps/detector.js';
 import { createLlmProvider } from '../llm/provider.js';
-import { resolveAbs, projectWikiPath as defaultProjectWikiPath, projectDbPath as defaultProjectDbPath, personalWikiPath as defaultPersonalWikiPath, personalDbPath as defaultPersonalDbPath, } from '../paths.js';
+import { resolveAbs, resolveProjectRoot, projectWikiPath as defaultProjectWikiPath, projectDbPath as defaultProjectDbPath, personalWikiPath as defaultPersonalWikiPath, personalDbPath as defaultPersonalDbPath, } from '../paths.js';
 import { queryRecentlySuperseded } from './claims.js';
 import { contradictionScan } from './contradiction.js';
 import { createProgressReporter } from './progress.js';
@@ -21,7 +21,7 @@ const GAP_MENTION_THRESHOLD = 10;
 const MIN_TOPIC_LENGTH = 5; // filter out short tokens (D42 tightened from 4)
 export async function auditWikiCommand(opts) {
     const scope = opts.scope ?? 'project';
-    const projectRoot = resolveAbs(opts.projectRoot ?? process.cwd());
+    const projectRoot = resolveProjectRoot(opts.projectRoot);
     const wikiPath = scope === 'personal'
         ? defaultPersonalWikiPath()
         : defaultProjectWikiPath(projectRoot);

package/dist/cli/audit-wiki.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/cli/contradiction-cli.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/cli/contradiction-cli.js CHANGED Viewed

@@ -1,13 +1,13 @@
 import { closeDb, openDb } from '../db/client.js';
 import { createLlmProvider } from '../llm/provider.js';
-import { resolveAbs, projectWikiPath as defaultProjectWikiPath, projectDbPath as defaultProjectDbPath, personalWikiPath as defaultPersonalWikiPath, personalDbPath as defaultPersonalDbPath, } from '../paths.js';
+import { resolveAbs, resolveProjectRoot, projectWikiPath as defaultProjectWikiPath, projectDbPath as defaultProjectDbPath, personalWikiPath as defaultPersonalWikiPath, personalDbPath as defaultPersonalDbPath, } from '../paths.js';
 import { contradictionScan } from './contradiction.js';
 /**
  * CLI wrapper for the contradiction scan command.
  * Sets up DB connection and LLM provider, runs the scan, cleans up.
  */
 export async function contradictionScanCommand(opts) {
-    const projectRoot = resolveAbs(opts.projectRoot ?? process.cwd());
+    const projectRoot = resolveProjectRoot(opts.projectRoot);
     const wikiPath = opts.scope === 'personal'
         ? defaultPersonalWikiPath()
         : defaultProjectWikiPath(projectRoot);

package/dist/cli/contradiction-cli.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/cli/crystallize.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/cli/crystallize.js CHANGED Viewed

@@ -4,7 +4,7 @@ import { join, relative } from 'node:path';
 import { closeDb, openDb } from '../db/client.js';
 import { countTokens } from '../gate/budget.js';
 import { createLlmProvider } from '../llm/provider.js';
-import { resolveAbs, projectWikiPath as defaultProjectWikiPath, projectDbPath as defaultProjectDbPath, } from '../paths.js';
+import { resolveAbs, resolveProjectRoot, projectWikiPath as defaultProjectWikiPath, projectDbPath as defaultProjectDbPath, } from '../paths.js';
 // ---------------------------------------------------------------------------
 // Constants
 // ---------------------------------------------------------------------------
@@ -221,7 +221,7 @@ function getWikiContext(bundle) {
 // Main: crystallize (direct wiki write)
 // ---------------------------------------------------------------------------
 export async function crystallizeCommand(opts) {
-    const projectRoot = resolveAbs(opts.projectRoot ?? process.cwd());
+    const projectRoot = resolveProjectRoot(opts.projectRoot);
     const wikiRoot = defaultProjectWikiPath(projectRoot);
     // 1. Git diff
     let gitResult;

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package/dist/cli/index.js CHANGED Viewed

@@ -4,7 +4,8 @@ import { auditWikiCommand } from './audit-wiki.js';
 import { contradictionScanCommand } from './contradiction-cli.js';
 import { crystallizeCommand } from './crystallize.js';
 import { loadIgnorePatterns, cleanIgnoredFromWiki } from '../init/ignore.js';
-import { resolveAbs, projectWikiPath as defaultProjectWikiPath, } from '../paths.js';
+import { reconcileStrayPinakesDirs } from '../init/reconcile.js';
+import { resolveProjectRoot, projectWikiPath as defaultProjectWikiPath, } from '../paths.js';
 import { exportCommand, renderExport } from './export.js';
 import { importCommand, renderImport } from './import.js';
 import { purgeCommand, renderPurge } from './purge.js';
@@ -118,7 +119,7 @@ async function main() {
             break;
         }
         case 'clean-wiki': {
-            const projectRoot = resolveAbs(getString(flags, 'project-root') ?? process.cwd());
+            const projectRoot = resolveProjectRoot(getString(flags, 'project-root'));
             const wikiRoot = defaultProjectWikiPath(projectRoot);
             const patterns = loadIgnorePatterns(projectRoot);
             const removed = cleanIgnoredFromWiki(wikiRoot, patterns);
@@ -126,6 +127,24 @@ async function main() {
             console.log(`Removed ${removed} ignored file(s) from wiki.`);
             break;
         }
+        case 'reconcile': {
+            const projectRoot = resolveProjectRoot(getString(flags, 'project-root'));
+            const wikiRoot = defaultProjectWikiPath(projectRoot);
+            const result = reconcileStrayPinakesDirs(projectRoot, wikiRoot);
+            if (result.strays.length === 0) {
+                // eslint-disable-next-line no-console
+                console.log(`No stray .pinakes directories found under ${projectRoot}.`);
+            }
+            else {
+                for (const stray of result.strays) {
+                    // eslint-disable-next-line no-console
+                    console.log(`${stray.strayPath}: recovered ${stray.filesRecovered.length} file(s), ` +
+                        `skipped ${stray.filesSkipped.length} (already existed), ` +
+                        `removed=${stray.removed}`);
+                }
+            }
+            break;
+        }
         case 'purge': {
             const scope = getRequiredString(flags, 'scope');
             const result = purgeCommand({
@@ -237,6 +256,7 @@ Usage:
   pinakes audit              [--n <count>] [--scope project|personal] [--project-root <dir>] [--db-path <path>]
   pinakes audit-wiki         [--project-root <dir>] [--db-path <path>]
   pinakes clean-wiki         [--project-root <dir>]
+  pinakes reconcile          [--project-root <dir>]
   pinakes purge              --scope <project|personal> --confirm [--project-root <dir>] [--db-path <path>]
   pinakes export             --scope <project|personal> [--out file.json] [--project-root <dir>] [--db-path <path>]
   pinakes import             --scope <project|personal> --in file.json [--project-root <dir>] [--db-path <path>]

package/dist/cli/index.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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package/dist/cli/rebuild.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
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1	+ {"version":3,"file":"rebuild.d.ts","sourceRoot":"","sources":["../../src/cli/rebuild.ts"],"names":[],"mappings":"AAkBA,OAAO,EAAwB,KAAK,QAAQ,EAAE,MAAM,0BAA0B,CAAC;AAE/E;;;;;;;;;;;;;;;;;;GAkBG;AAEH,MAAM,WAAW,cAAc;IAC7B,2FAA2F;IAC3F,WAAW,CAAC,EAAE,MAAM,CAAC;IACrB,iFAAiF;IACjF,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,2DAA2D;IAC3D,WAAW,CAAC,EAAE,MAAM,CAAC;IACrB,0DAA0D;IAC1D,aAAa,CAAC,EAAE,MAAM,CAAC;IACvB,iIAAiI;IACjI,KAAK,CAAC,EAAE,SAAS,GAAG,UAAU,GAAG,MAAM,CAAC;IACxC;;;OAGG;IACH,QAAQ,CAAC,EAAE,QAAQ,CAAC;CACrB;AAED,MAAM,WAAW,cAAc;IAC7B,KAAK,EAAE,SAAS,GAAG,UAAU,CAAC;IAC9B,KAAK,EAAE,MAAM,CAAC;IACd,KAAK,EAAE,MAAM,CAAC;IACd,YAAY,EAAE,MAAM,CAAC;IACrB,cAAc,EAAE,MAAM,CAAC;IACvB,cAAc,EAAE,MAAM,CAAC;IACvB,UAAU,EAAE,MAAM,CAAC;CACpB;AAED;;;;;GAKG;AACH,wBAAsB,cAAc,CAAC,OAAO,EAAE,cAAc,GAAG,OAAO,CAAC,cAAc,EAAE,CAAC,CA6CvF"}

package/dist/cli/rebuild.js CHANGED Viewed

@@ -4,7 +4,7 @@ import { IngesterService } from '../ingest/ingester.js';
 import { listMarkdownFiles } from '../ingest/manifest.js';
 import { logger } from '../observability/logger.js';
 import { resolve } from 'node:path';
-import { resolveAbs, projectWikiPath as defaultProjectWikiPath, projectDbPath as defaultProjectDbPath, personalWikiPath as defaultPersonalWikiPath, personalDbPath as defaultPersonalDbPath, projectDataDir, pinakesRoot, } from '../paths.js';
+import { resolveAbs, resolveProjectRoot, projectWikiPath as defaultProjectWikiPath, projectDbPath as defaultProjectDbPath, personalWikiPath as defaultPersonalWikiPath, personalDbPath as defaultPersonalDbPath, projectDataDir, pinakesRoot, } from '../paths.js';
 import { TransformersEmbedder } from '../retrieval/embedder.js';
 /**
  * Run a full-rebuild against one or both scopes. Returns a list of summaries
@@ -14,7 +14,7 @@ import { TransformersEmbedder } from '../retrieval/embedder.js';
  */
 export async function rebuildCommand(options) {
     const summaries = [];
-    const projectRoot = resolveAbs(options.projectRoot ?? process.cwd());
+    const projectRoot = resolveProjectRoot(options.projectRoot);
     const projectWiki = defaultProjectWikiPath(projectRoot);
     if (!existsSync(projectWiki)) {
         throw new Error(`wiki path does not exist: ${projectWiki}`);

package/dist/cli/rebuild.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/cli/serve.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/cli/serve.js CHANGED Viewed

@@ -11,11 +11,12 @@ import { ChokidarWatcher } from '../ingest/chokidar.js';
 import { scanRepoMarkdownFiles } from '../init/scanner.js';
 import { copyMarkdownToWiki } from '../init/copy.js';
 import { ensurePinakesIgnoreFile } from '../init/ignore.js';
+import { reconcileStrayPinakesDirs } from '../init/reconcile.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, legacyProjectWikiPath, ensurePinakesGitignore, ensureAgentInstructions, } from '../paths.js';
+import { resolveAbs, resolveProjectRoot, projectWikiPath as defaultProjectWikiPath, projectDbPath as defaultProjectDbPath, projectAuditJsonlPath, personalWikiPath as defaultPersonalWikiPath, personalDbPath as defaultPersonalDbPath, personalAuditJsonlPath, projectDataDir, pinakesRoot, legacyProjectWikiPath, ensurePinakesGitignore, ensureAgentInstructions, } from '../paths.js';
 import { writeAuditRow } from '../observability/audit.js';
 import { child, logger } from '../observability/logger.js';
 import { installSighupHandler, metrics } from '../observability/metrics.js';
@@ -27,7 +28,7 @@ import { QuickJSExecutor } from '../sandbox/executor.js';
  * through the CLI argv path.
  */
 export async function buildServer(options) {
-    const projectRoot = resolveAbs(options.projectRoot ?? process.cwd());
+    const projectRoot = resolveProjectRoot(options.projectRoot);
     // Ensure .pinakes/.gitignore, .pinakesignore, and agent instructions exist
     ensurePinakesGitignore(projectRoot);
     ensurePinakesIgnoreFile(projectRoot);
@@ -35,6 +36,18 @@ export async function buildServer(options) {
     // Migrate wiki from old centralized location to in-repo path
     migrateLegacyWikiToInRepo(projectRoot);
     const projectWiki = defaultProjectWikiPath(projectRoot);
+    // Recover stray `.pinakes/` dirs left behind by earlier subdir-cwd invocations.
+    // Runs before the wiki bootstrap so recovered files land in the canonical wiki
+    // even on a fresh project.
+    const reconciled = reconcileStrayPinakesDirs(projectRoot, projectWiki);
+    for (const stray of reconciled.strays) {
+        logger.warn({
+            strayPath: stray.strayPath,
+            filesRecovered: stray.filesRecovered.length,
+            filesSkipped: stray.filesSkipped.length,
+            removed: stray.removed,
+        }, 'reconciled stray .pinakes directory — markdown moved under wiki/recovered/');
+    }
     if (!existsSync(projectWiki)) {
         // First run only — bootstrap the wiki from repo markdown, then hand
         // ownership to `.pinakes/wiki/`. There is no continuous repo → wiki sync.
@@ -205,7 +218,7 @@ export async function buildServer(options) {
  * handlers, listen forever.
  */
 export async function serveCommand(options) {
-    logger.info({ projectRoot: options.projectRoot ?? process.cwd() }, 'pinakes starting');
+    logger.info({ projectRoot: resolveProjectRoot(options.projectRoot) }, 'pinakes starting');
     installSighupHandler();
     const { server, shutdown } = await buildServer(options);
     const transport = new StdioServerTransport();

package/dist/cli/serve.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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package/dist/init/reconcile.d.ts ADDED Viewed

@@ -0,0 +1,26 @@
+export interface StrayReport {
+    strayPath: string;
+    filesRecovered: string[];
+    filesSkipped: string[];
+    removed: boolean;
+}
+export interface ReconcileResult {
+    strays: StrayReport[];
+}
+/**
+ * Walk the project tree looking for accidental `.pinakes/` directories in
+ * subdirectories. These happen when an MCP client launches pinakes with cwd
+ * set to a subdir (and no absolute `--project-root`), so the server bootstraps
+ * a second wiki in the wrong place.
+ *
+ * For each stray found:
+ *   - If its `wiki/` has any markdown, copy the files into
+ *     `<canonicalWiki>/recovered/<relative-path-to-stray>/...`, never
+ *     overwriting existing files.
+ *   - Delete the stray `.pinakes/` directory entirely.
+ *
+ * Subdirectories that contain their own `.git` are skipped (they are
+ * standalone subprojects — their `.pinakes/` is legitimate).
+ */
+export declare function reconcileStrayPinakesDirs(projectRoot: string, canonicalWiki: string): ReconcileResult;
+//# sourceMappingURL=reconcile.d.ts.map

package/dist/init/reconcile.d.ts.map ADDED Viewed

@@ -0,0 +1 @@

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package/dist/init/reconcile.js ADDED Viewed

@@ -0,0 +1,139 @@
+import { cpSync, existsSync, mkdirSync, readdirSync, rmSync, statSync } from 'node:fs';
+import { basename, dirname, relative, resolve } from 'node:path';
+import { logger } from '../observability/logger.js';
+const SKIP_DIRS = new Set([
+    'node_modules',
+    'target',
+    'dist',
+    'build',
+    '.git',
+    '.pnpm',
+    '.venv',
+    'venv',
+    '.next',
+    '.turbo',
+    '.cache',
+    'coverage',
+    'vendor',
+]);
+const MAX_DEPTH = 8;
+/**
+ * Walk the project tree looking for accidental `.pinakes/` directories in
+ * subdirectories. These happen when an MCP client launches pinakes with cwd
+ * set to a subdir (and no absolute `--project-root`), so the server bootstraps
+ * a second wiki in the wrong place.
+ *
+ * For each stray found:
+ *   - If its `wiki/` has any markdown, copy the files into
+ *     `<canonicalWiki>/recovered/<relative-path-to-stray>/...`, never
+ *     overwriting existing files.
+ *   - Delete the stray `.pinakes/` directory entirely.
+ *
+ * Subdirectories that contain their own `.git` are skipped (they are
+ * standalone subprojects — their `.pinakes/` is legitimate).
+ */
+export function reconcileStrayPinakesDirs(projectRoot, canonicalWiki) {
+    const result = { strays: [] };
+    const canonicalPinakes = resolve(projectRoot, '.pinakes');
+    walk(projectRoot, projectRoot, canonicalPinakes, canonicalWiki, 0, result);
+    return result;
+}
+function walk(projectRoot, current, canonicalPinakes, canonicalWiki, depth, result) {
+    if (depth > MAX_DEPTH)
+        return;
+    let entries;
+    try {
+        entries = readdirSync(current);
+    }
+    catch {
+        return;
+    }
+    for (const name of entries) {
+        if (SKIP_DIRS.has(name))
+            continue;
+        const full = resolve(current, name);
+        let stat;
+        try {
+            stat = statSync(full);
+        }
+        catch {
+            continue;
+        }
+        if (!stat.isDirectory())
+            continue;
+        // Found a `.pinakes/` — is it the canonical one or a stray?
+        if (name === '.pinakes') {
+            if (full === canonicalPinakes)
+                continue;
+            result.strays.push(recoverStray(full, projectRoot, canonicalWiki));
+            continue;
+        }
+        // Subdir with its own `.git` is a nested repo — leave it alone.
+        if (existsSync(resolve(full, '.git')))
+            continue;
+        walk(projectRoot, full, canonicalPinakes, canonicalWiki, depth + 1, result);
+    }
+}
+function recoverStray(strayPath, projectRoot, canonicalWiki) {
+    const report = {
+        strayPath,
+        filesRecovered: [],
+        filesSkipped: [],
+        removed: false,
+    };
+    const strayWiki = resolve(strayPath, 'wiki');
+    if (existsSync(strayWiki)) {
+        const relStray = relative(projectRoot, resolve(strayPath, '..'));
+        const recoveredRoot = resolve(canonicalWiki, 'recovered', relStray || basename(strayPath));
+        copyTree(strayWiki, recoveredRoot, '', report);
+    }
+    try {
+        rmSync(strayPath, { recursive: true, force: true });
+        report.removed = true;
+    }
+    catch (err) {
+        logger.warn({ err, strayPath }, 'failed to remove stray .pinakes dir');
+    }
+    return report;
+}
+function copyTree(srcDir, dstDir, relPrefix, report) {
+    let entries;
+    try {
+        entries = readdirSync(srcDir);
+    }
+    catch {
+        return;
+    }
+    for (const name of entries) {
+        const src = resolve(srcDir, name);
+        const dst = resolve(dstDir, name);
+        const rel = relPrefix ? `${relPrefix}/${name}` : name;
+        let stat;
+        try {
+            stat = statSync(src);
+        }
+        catch {
+            continue;
+        }
+        if (stat.isDirectory()) {
+            copyTree(src, dst, rel, report);
+            continue;
+        }
+        if (!name.endsWith('.md'))
+            continue;
+        if (existsSync(dst)) {
+            report.filesSkipped.push(rel);
+            continue;
+        }
+        try {
+            mkdirSync(dirname(dst), { recursive: true });
+            cpSync(src, dst);
+            report.filesRecovered.push(rel);
+        }
+        catch (err) {
+            logger.warn({ err, src, dst }, 'failed to recover stray wiki file');
+            report.filesSkipped.push(rel);
+        }
+    }
+}
+//# sourceMappingURL=reconcile.js.map

package/dist/init/reconcile.js.map ADDED Viewed

@@ -0,0 +1 @@

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package/dist/paths.d.ts CHANGED Viewed

@@ -24,6 +24,21 @@
  */
 /** Resolve a path to absolute, using cwd if relative. */
 export declare function resolveAbs(p: string): string;
+/**
+ * Walk up from `startDir` looking for a `.git` entry (file or directory —
+ * git worktrees represent `.git` as a file). Returns the first ancestor that
+ * contains one, or `null` if none is found before hitting the filesystem root.
+ */
+export declare function findGitRoot(startDir: string): string | null;
+/**
+ * Pick the canonical project root for a Pinakes invocation.
+ *
+ *   1. If `explicit` is provided (usually from `--project-root`), use it verbatim.
+ *   2. Otherwise, walk up from cwd looking for `.git` so subdir invocations
+ *      resolve to the same repo root and don't spawn a duplicate `.pinakes/`.
+ *   3. Fallback to cwd for non-git directories (scratch repos, test fixtures).
+ */
+export declare function resolveProjectRoot(explicit?: string): string;
 /**
  * Mangle an absolute path into a directory-safe name.
  * Uses Claude Code's convention: replace '/' with '-'.

package/dist/paths.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/paths.js CHANGED Viewed

@@ -24,7 +24,7 @@
  */
 import { existsSync, mkdirSync, readFileSync, writeFileSync } from 'node:fs';
 import { homedir } from 'node:os';
-import { isAbsolute, resolve } from 'node:path';
+import { dirname, isAbsolute, resolve } from 'node:path';
 // ---------------------------------------------------------------------------
 // Helpers
 // ---------------------------------------------------------------------------
@@ -32,6 +32,35 @@ import { isAbsolute, resolve } from 'node:path';
 export function resolveAbs(p) {
     return isAbsolute(p) ? p : resolve(process.cwd(), p);
 }
+/**
+ * Walk up from `startDir` looking for a `.git` entry (file or directory —
+ * git worktrees represent `.git` as a file). Returns the first ancestor that
+ * contains one, or `null` if none is found before hitting the filesystem root.
+ */
+export function findGitRoot(startDir) {
+    let current = resolveAbs(startDir);
+    while (true) {
+        if (existsSync(resolve(current, '.git')))
+            return current;
+        const parent = dirname(current);
+        if (parent === current)
+            return null;
+        current = parent;
+    }
+}
+/**
+ * Pick the canonical project root for a Pinakes invocation.
+ *
+ *   1. If `explicit` is provided (usually from `--project-root`), use it verbatim.
+ *   2. Otherwise, walk up from cwd looking for `.git` so subdir invocations
+ *      resolve to the same repo root and don't spawn a duplicate `.pinakes/`.
+ *   3. Fallback to cwd for non-git directories (scratch repos, test fixtures).
+ */
+export function resolveProjectRoot(explicit) {
+    if (explicit)
+        return resolveAbs(explicit);
+    return findGitRoot(process.cwd()) ?? process.cwd();
+}
 /**
  * Mangle an absolute path into a directory-safe name.
  * Uses Claude Code's convention: replace '/' with '-'.
@@ -173,6 +202,6 @@ export function resolveCliDbPath(options, scope) {
     }
     if (options.dbPath)
         return resolveAbs(options.dbPath);
-    return projectDbPath(options.projectRoot ?? process.cwd());
+    return projectDbPath(resolveProjectRoot(options.projectRoot));
 }
 //# sourceMappingURL=paths.js.map

package/dist/paths.js.map CHANGED Viewed

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package/package.json CHANGED Viewed

@@ -1,6 +1,6 @@
 {
   "name": "@pella-labs/pinakes",
-  "version": "0.6.1",
+  "version": "0.6.2",
   "description": "Local stdio MCP server that indexes a Karpathy-style two-level knowledge wiki into SQLite and exposes it to a coding LLM via Cloudflare-style code-mode.",
   "type": "module",
   "bin": {