@monoes/monomindcli 2.7.12 → 2.7.14

package/dist/src/commands/doc.js

@@ -3,7 +3,7 @@
  */
 import * as path from 'node:path';
 import { output } from '../output.js';
-import { getGlobalBrainDir } from '../memory/memory-bridge.js';
+import { getGlobalBrainDir, getProjectRoot } from '../memory/memory-bridge.js';
 const ingestCommand = {
     name: 'ingest',
     description: 'Ingest documents into the knowledge base',
@@ -25,14 +25,17 @@ const ingestCommand = {
         const fs = await import('node:fs');
         const resolved = path.resolve(target);
         // Zero-decision routing: an explicit --global wins; otherwise paths OUTSIDE
-        // the current project belong to the personal brain (a project store keyed
-        // to this cwd would never see them again from another project).
+        // this project belong to the personal brain (a project-scoped store would
+        // never surface them again from another project).
         let scope = String(ctx.flags.scope || 'shared');
         if (ctx.flags.global === true) {
             scope = 'global';
         }
         else if (!ctx.flags.scope) {
-            const relToCwd = path.relative(process.cwd(), resolved);
+            // Against the PROJECT ROOT, not the cwd: from a package subdirectory,
+            // `doc ingest ../../docs` targets this very project, and routing it to
+            // the personal brain because it sits above the cwd is simply wrong.
+            const relToCwd = path.relative(getProjectRoot(ctx.cwd || process.cwd()), resolved);
             if (relToCwd.startsWith('..') || path.isAbsolute(relToCwd)) {
                 scope = 'global';
                 output.writeln(output.dim(`  ${target} is outside this project — ingesting into the global brain (use --scope shared to force project scope)`));
@@ -44,7 +47,7 @@ const ingestCommand = {
             const stat = fs.statSync(resolved);
             if (stat.isDirectory()) {
                 const result = await ingestDirectory(resolved, scope, {
-                    rootDir: ctx.cwd || process.cwd(),
+                    rootDir: getProjectRoot(ctx.cwd || process.cwd()),
                     onProgress: (file, done, total) => {
                         spinner.setText(`[${done + 1}/${total}] ${path.basename(file)}`);
                     },
@@ -192,7 +195,7 @@ const listDocCommand = {
         const { listDocuments } = await import('../knowledge/document-pipeline.js');
         const isGlobal = ctx.flags.global === true;
         const scope = isGlobal ? 'global' : ctx.flags.scope ? String(ctx.flags.scope) : undefined;
-        const docs = listDocuments(isGlobal ? getGlobalBrainDir() : process.cwd(), scope);
+        const docs = listDocuments(isGlobal ? getGlobalBrainDir() : getProjectRoot(), scope);
         if (!docs.length) {
             output.writeln(output.dim('No documents indexed. Run: monomind doc ingest <path>'));
             return { success: true, data: [] };
@@ -226,7 +229,7 @@ const exportDocCommand = {
         const spinner = output.createSpinner({ text: 'Exporting to OKF...' });
         spinner.start();
         try {
-            const result = await exportToOKF(outDir, isGlobal ? getGlobalBrainDir() : process.cwd(), scope);
+            const result = await exportToOKF(outDir, isGlobal ? getGlobalBrainDir() : getProjectRoot(), scope);
             spinner.succeed(`Exported ${result.exported} documents to ${result.outputDir}`);
             return { success: true, data: result };
         }
@@ -236,17 +239,254 @@ const exportDocCommand = {
         }
     },
 };
+const removeDocCommand = {
+    name: 'remove',
+    description: 'Forget an indexed document',
+    aliases: ['rm', 'forget'],
+    options: [
+        { name: 'scope', short: 's', description: 'Knowledge scope (default: shared)', type: 'string', default: 'shared' },
+        { name: 'global', short: 'g', description: 'Remove from the personal cross-project global brain', type: 'boolean' },
+    ],
+    examples: [
+        { command: 'monomind doc remove ./docs/old-spec.md', description: 'Stop returning a document in search' },
+        { command: 'monomind doc remove ~/notes/stale.md --global', description: 'Forget it from the personal brain' },
+    ],
+    action: async (ctx) => {
+        const target = ctx.args[0];
+        if (!target) {
+            output.printError('Document path required: monomind doc remove <path>');
+            return { success: false, exitCode: 1 };
+        }
+        const { listDocuments, removeDocument } = await import('../knowledge/document-pipeline.js');
+        const isGlobal = ctx.flags.global === true;
+        const scope = isGlobal ? 'global' : String(ctx.flags.scope || 'shared');
+        const root = isGlobal ? getGlobalBrainDir() : getProjectRoot();
+        const resolved = path.resolve(target);
+        // The metadata log keys on the resolved path recorded at ingest, so a
+        // mistyped path would otherwise write a tombstone that matches nothing and
+        // report success. Fail like `rm` does instead.
+        if (!listDocuments(root, scope).some(d => path.resolve(d.filePath) === resolved)) {
+            output.printError(`Not indexed under scope '${scope}': ${resolved}`);
+            output.writeln(output.dim(`  See what is indexed: monomind doc list${isGlobal ? ' --global' : ''}`));
+            return { success: false, exitCode: 1 };
+        }
+        await removeDocument(resolved, scope, root);
+        output.writeln(`Forgot ${output.highlight(path.basename(resolved))} (${scope})`);
+        // Honest about what happened on disk: the tombstone hides the chunks from
+        // every search surface, but the bridge exposes no delete-by-prefix, so the
+        // rows themselves go on the next full re-index.
+        output.writeln(output.dim('  Chunks are hidden from search immediately; storage is reclaimed on the next full re-index.'));
+        return { success: true, data: { filePath: resolved, scope } };
+    },
+};
+const reconcileDocCommand = {
+    name: 'reconcile',
+    description: 'Find and forget indexed documents whose source file no longer exists',
+    options: [
+        { name: 'scope', short: 's', description: 'Knowledge scope (default: shared)', type: 'string', default: 'shared' },
+        { name: 'global', short: 'g', description: 'Reconcile the personal cross-project global brain', type: 'boolean' },
+        { name: 'apply', description: 'Actually forget the stale entries (default: dry run)', type: 'boolean' },
+    ],
+    examples: [
+        { command: 'monomind doc reconcile', description: 'Show indexed documents whose file is gone (changes nothing)' },
+        { command: 'monomind doc reconcile --apply', description: 'Forget them' },
+        { command: 'monomind doc reconcile --global --apply', description: 'Same, for the personal brain' },
+    ],
+    action: async (ctx) => {
+        const { reconcileIndex } = await import('../knowledge/document-pipeline.js');
+        const isGlobal = ctx.flags.global === true;
+        const scope = isGlobal ? 'global' : String(ctx.flags.scope || 'shared');
+        const root = isGlobal ? getGlobalBrainDir() : getProjectRoot();
+        const apply = ctx.flags.apply === true;
+        let report;
+        try {
+            report = await reconcileIndex(root, { scope, apply });
+        }
+        catch (err) {
+            // reconcileIndex refuses to run against a missing root or a missing
+            // metadata log, because there every indexed file looks deleted. Surface
+            // that as a refusal, never as "0 stale entries found".
+            output.printError(String(err instanceof Error ? err.message : err));
+            return { success: false, exitCode: 1 };
+        }
+        if (report.missing.length === 0) {
+            output.writeln(`Index is consistent — all ${report.scanned} indexed documents still exist.`);
+            return { success: true, data: report };
+        }
+        output.writeln(`${output.highlight(String(report.missing.length))} of ${report.scanned} indexed documents no longer exist on disk:`);
+        for (const m of report.missing.slice(0, 20)) {
+            output.writeln(output.dim(`  ${m.filePath}`));
+        }
+        if (report.missing.length > 20) {
+            output.writeln(output.dim(`  ... and ${report.missing.length - 20} more`));
+        }
+        if (!apply) {
+            // Dry run is the default because "the file is missing" also describes an
+            // unmounted volume, a checked-out branch, and a partial clone. The user
+            // is the one who knows which it is.
+            output.writeln('');
+            output.writeln(output.dim('Nothing was changed. Re-run with --apply to forget these entries.'));
+            return { success: true, data: report };
+        }
+        output.writeln('');
+        output.writeln(`Forgot ${output.highlight(String(report.removed))} stale ${report.removed === 1 ? 'entry' : 'entries'}.`);
+        if (report.archivePath) {
+            output.writeln(output.dim(`  Archived first, and reversible from: ${report.archivePath}`));
+        }
+        output.writeln(output.dim('  Chunks are hidden from search immediately; storage is reclaimed on the next full re-index.'));
+        return { success: true, data: report };
+    },
+};
+const importDocCommand = {
+    name: 'import',
+    description: 'Import an OKF bundle produced by `doc export`',
+    options: [
+        { name: 'scope', short: 's', description: 'Knowledge scope (default: shared)', type: 'string', default: 'shared' },
+        { name: 'global', short: 'g', description: 'Import into the personal cross-project global brain', type: 'boolean' },
+    ],
+    examples: [
+        { command: 'monomind doc import ./.monomind/knowledge-export', description: 'Import a bundle into this project' },
+        { command: 'monomind doc import ~/brain-bundle --global', description: 'Restore a personal brain on another machine' },
+    ],
+    action: async (ctx) => {
+        const bundle = ctx.args[0];
+        if (!bundle) {
+            output.printError('Bundle directory required: monomind doc import <bundle-dir>');
+            return { success: false, exitCode: 1 };
+        }
+        const { importFromOKF } = await import('../knowledge/document-pipeline.js');
+        const fs = await import('node:fs');
+        const resolved = path.resolve(bundle);
+        if (!fs.existsSync(resolved) || !fs.statSync(resolved).isDirectory()) {
+            output.printError(`Not a directory: ${resolved}`);
+            return { success: false, exitCode: 1 };
+        }
+        const isGlobal = ctx.flags.global === true;
+        const scope = isGlobal ? 'global' : String(ctx.flags.scope || 'shared');
+        const spinner = output.createSpinner({ text: 'Importing OKF bundle...' });
+        spinner.start();
+        try {
+            // importFromOKF, not ingestDirectory: the bundle's own index.md is a
+            // manifest, not knowledge, and plain ingest would index it as a document.
+            const result = await importFromOKF(resolved, scope, isGlobal ? getGlobalBrainDir() : getProjectRoot());
+            spinner.succeed(`Imported ${result.totalChunks} chunks from ${result.filesProcessed} documents (${result.filesSkipped} already indexed)`);
+            if (result.errors.length) {
+                output.writeln(output.dim(`  Errors: ${result.errors.length}`));
+                for (const err of result.errors.slice(0, 5))
+                    output.writeln(output.dim(`    ${err}`));
+            }
+            return { success: true, data: result };
+        }
+        catch (err) {
+            spinner.fail(String(err));
+            return { success: false, exitCode: 1 };
+        }
+    },
+};
+const evalCommand = {
+    name: 'eval',
+    description: 'Measure retrieval quality (Recall@1/5/10, MRR@10) on the local golden set',
+    aliases: ['benchmark', 'scoreboard'],
+    options: [
+        { name: 'split', description: "Golden-set split: dev (tunable) | test (sealed, stop-condition only) | all", type: 'string', default: 'dev' },
+        { name: 'k', description: 'Retrieval cutoff (default: 10)', type: 'number', default: 10 },
+        { name: 'json', description: 'Emit the machine-readable report only', type: 'boolean' },
+        { name: 'out', short: 'o', description: 'Write the JSON report to this path', type: 'string' },
+        { name: 'rebuild', description: 'Rebuild the isolated eval store from scratch', type: 'boolean' },
+        { name: 'screen', description: 'Screen a JSON file of candidate golden pairs for lexical overlap before adding them', type: 'string' },
+        { name: 'provision-model', description: 'Download the embedding weights (the ONLY networked step; run once before evaluating)', type: 'boolean' },
+        { name: 'store-root', description: 'Where the isolated eval store lives (default: <repo>/.monomind/eval)', type: 'string' },
+    ],
+    examples: [
+        { command: 'monomind doc eval', description: 'Score the dev split and print the table' },
+        { command: 'monomind doc eval --split test --json', description: 'Sealed run — aggregates only, appended to the exposure ledger' },
+        { command: 'monomind doc eval --provision-model', description: 'One-off: fetch the embedding weights (the only networked step)' },
+        { command: 'monomind doc eval --out scoreboard.json', description: 'Persist the machine-readable report' },
+    ],
+    action: async (ctx) => {
+        const { runEval, renderReport } = await import('../knowledge/eval/harness.js');
+        // Authoring-time screening: reject high-overlap candidates BEFORE they
+        // enter the set, rather than discovering the distribution afterwards.
+        if (ctx.flags.screen) {
+            const fs = await import('node:fs');
+            const { screenCandidates } = await import('../knowledge/eval/harness.js');
+            const cands = JSON.parse(fs.readFileSync(String(ctx.flags.screen), 'utf8'));
+            const rep = await screenCandidates(getProjectRoot(ctx.cwd || process.cwd()), cands);
+            if (ctx.flags.out)
+                fs.writeFileSync(String(ctx.flags.out), JSON.stringify(rep, null, 2));
+            if (ctx.flags.json === true) {
+                output.writeln(JSON.stringify(rep, null, 2));
+                return { success: true, data: rep };
+            }
+            output.writeln(`\nscreened ${rep.total}: ${rep.accepted} accepted, ${rep.rejected} rejected (corpus ${rep.corpusHash})`);
+            output.writeln(`overlap bands of accepted: low ${rep.bands.low}  mid ${rep.bands.mid}  high ${rep.bands.high}`);
+            for (const c of rep.candidates.filter(x => !x.accepted))
+                output.writeln(`  REJECT ${c.id}: ${c.reason}`);
+            return { success: true, data: rep };
+        }
+        // The explicit, non-query-time provisioning step. Separating this from
+        // measurement is what makes "clean checkout" and "zero network at query
+        // time" jointly satisfiable — `doc eval` itself never fetches.
+        if (ctx.flags['provision-model'] === true) {
+            const { provisionModel } = await import('../knowledge/eval/model-presence.js');
+            try {
+                const p = await provisionModel(m => output.writeln(output.dim('  ' + m)));
+                output.printSuccess(`Embedding model provisioned (${(p.bytes / 1e6).toFixed(0)}MB).`);
+                return { success: true, data: p };
+            }
+            catch (err) {
+                output.printError(String(err instanceof Error ? err.message : err));
+                return { success: false, exitCode: 1 };
+            }
+        }
+        const split = String(ctx.flags.split || 'dev');
+        if (!['dev', 'test', 'all'].includes(split)) {
+            output.printError(`--split must be dev, test or all (got "${split}")`);
+            return { success: false, exitCode: 1 };
+        }
+        const asJson = ctx.flags.json === true;
+        const repoRoot = getProjectRoot(ctx.cwd || process.cwd());
+        try {
+            const report = await runEval({
+                repoRoot,
+                k: Number(ctx.flags.k || 10),
+                rebuild: ctx.flags.rebuild === true,
+                storeRoot: ctx.flags['store-root'] ? String(ctx.flags['store-root']) : undefined,
+                split: split,
+                onProgress: (msg) => { if (!asJson)
+                    output.writeln(output.dim('  ' + msg)); },
+            });
+            if (ctx.flags.out) {
+                const fs = await import('node:fs');
+                fs.writeFileSync(String(ctx.flags.out), JSON.stringify(report, null, 2));
+            }
+            if (asJson)
+                output.writeln(JSON.stringify(report, null, 2));
+            else
+                output.writeln(renderReport(report));
+            // A network attempt during the query phase invalidates the run outright.
+            return { success: report.networkFree.verdict === 'proven-blocked', data: report };
+        }
+        catch (err) {
+            output.printError(String(err instanceof Error ? err.message : err));
+            return { success: false, exitCode: 1 };
+        }
+    },
+};
 export const docCommand = {
     name: 'doc',
     description: 'Second Brain — document knowledge management',
     aliases: ['docs', 'knowledge'],
-    subcommands: [ingestCommand, searchDocCommand, listDocCommand, exportDocCommand],
+    subcommands: [ingestCommand, searchDocCommand, listDocCommand, exportDocCommand, importDocCommand, removeDocCommand, reconcileDocCommand, evalCommand],
     options: [],
     examples: [
         { command: 'monomind doc ingest ./docs', description: 'Index documents' },
         { command: 'monomind doc search -q "auth flow"', description: 'Semantic search' },
         { command: 'monomind doc list', description: 'List indexed docs' },
         { command: 'monomind doc export', description: 'Export as OKF bundle' },
+        { command: 'monomind doc import ./bundle', description: 'Import an OKF bundle' },
+        { command: 'monomind doc remove ./docs/old.md', description: 'Forget an indexed document' },
+        { command: 'monomind doc eval', description: 'Score retrieval quality on the golden set' },
     ],
     action: async () => {
         output.writeln();
@@ -260,6 +500,9 @@ export const docCommand = {
             `${output.highlight('search')}  - Semantic search over indexed documents`,
             `${output.highlight('list')}    - List indexed documents`,
             `${output.highlight('export')}  - Export as OKF bundle (markdown + frontmatter)`,
+            `${output.highlight('import')}  - Import an OKF bundle produced by export`,
+            `${output.highlight('remove')}  - Forget an indexed document (aliases: rm, forget)`,
+            `${output.highlight('eval')}    - Retrieval-quality scoreboard: Recall@1/5/10, MRR@10`,
         ]);
         return { success: true };
     },

package/dist/src/commands/doc.js.map

@@ -1 +1 @@
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package/dist/src/commands/doctor-project-checks.d.ts

@@ -10,9 +10,10 @@ export declare function checkMemoryDatabase(): Promise<HealthCheck>;
  * from sessions and org runs. Informational — an empty graph on a fresh
  * project is normal, so it never fails. */
 export declare function checkMemoryKnowledgeGraph(): Promise<HealthCheck>;
-/** Second Brain: when this project has an indexed knowledge base, semantic
- * search needs the local embedding model. Its absence is silent (search
- * degrades to keyword matching) — surface it here instead. */
+/** Second Brain: when there is any indexed knowledge — ingested docs in this
+ * project, the personal global brain, or the monograph god-node chunk —
+ * semantic search needs the local embedding model. Its absence is silent
+ * (search degrades to keyword matching), so surface it here instead. */
 export declare function checkSecondBrainModel(): Promise<HealthCheck>;
 export declare function checkApiKeys(): Promise<HealthCheck>;
 export declare function checkMcpServers(): Promise<HealthCheck>;
@@ -43,4 +44,25 @@ export declare function checkSecurityAuditFindings(): Promise<HealthCheck>;
  * AutoMem proficiency check — reports memory learning health
  */
 export declare function checkMemoryProficiency(): Promise<HealthCheck>;
+/** AppleDouble sidecars (`._name`) under `.claude/`.
+ *
+ * macOS writes these whenever a file carrying extended attributes is copied to
+ * a filesystem that cannot store them natively — exFAT, most USB/network
+ * volumes. Harmless as data, but Claude Code discovers skills and commands by
+ * reading `.claude/skills/` and `.claude/commands/`, and a stray
+ * `._createorg.md` is registered as a real command: a garbage entry named
+ * `mastermind:._createorg` appears in the roster, and its "content" is a binary
+ * resource fork. They also reappear after any Finder copy, `cp`, or tar
+ * extract, so a one-time delete does not hold.
+ *
+ * Reported here rather than swept silently, because deleting files under
+ * `.claude/` should be something the operator sees. `doctor --fix` removes them.
+ */
+export declare function checkAppleDoubleSidecars(): Promise<HealthCheck>;
+/** Every `._*` file under the project's `.claude/` trees. Both the repo-root
+ *  tree and the npm-shipped copy under packages/, since a sidecar in the latter
+ *  ships to users. */
+export declare function findAppleDoubleSidecars(cwd: string): string[];
+/** Delete every AppleDouble sidecar found. Returns how many were removed. */
+export declare function fixAppleDoubleSidecars(cwd: string): number;
 //# sourceMappingURL=doctor-project-checks.d.ts.map

package/dist/src/commands/doctor-project-checks.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"doctor-project-checks.d.ts","sourceRoot":"","sources":["../../../src/commands/doctor-project-checks.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAOH,OAAO,KAAK,EAAE,WAAW,EAAE,MAAM,wBAAwB,CAAC;AAS1D,YAAY,EAAE,WAAW,EAAE,CAAC;AAE5B,wBAAsB,eAAe,IAAI,OAAO,CAAC,WAAW,CAAC,CAiB5D;AAED,wBAAsB,mBAAmB,IAAI,OAAO,CAAC,WAAW,CAAC,CAahE;AAED;;2CAE2C;AAC3C,wBAAsB,yBAAyB,IAAI,OAAO,CAAC,WAAW,CAAC,CAkBtE;AAaD;;;wEAGwE;AACxE,wBAAsB,qBAAqB,IAAI,OAAO,CAAC,WAAW,CAAC,CA4ClE;AAED,wBAAsB,YAAY,IAAI,OAAO,CAAC,WAAW,CAAC,CAyBzD;AAED,wBAAsB,eAAe,IAAI,OAAO,CAAC,WAAW,CAAC,CAsB5D;AAED,wBAAsB,cAAc,IAAI,OAAO,CAAC,WAAW,CAAC,CA6B3D;AAED,wBAAsB,uBAAuB,IAAI,OAAO,CAAC,WAAW,CAAC,CA+BpE;AAED,wBAAsB,iBAAiB,IAAI,OAAO,CAAC,WAAW,CAAC,CAwB9D;AAoED,wBAAsB,eAAe,IAAI,OAAO,CAAC,OAAO,CAAC,CAiBxD;AAED,wBAAsB,iBAAiB,IAAI,OAAO,CAAC,WAAW,CAAC,CAa9D;AAoDD,wBAAsB,sBAAsB,IAAI,OAAO,CAAC,WAAW,CAAC,CAWnE;AAyCD,wBAAsB,sBAAsB,IAAI,OAAO,CAAC,WAAW,CAAC,CAiBnE;AA4BD;6EAC6E;AAC7E,wBAAsB,oBAAoB,IAAI,OAAO,CAAC,OAAO,CAAC,CAoB7D;AAED,wBAAsB,kBAAkB,IAAI,OAAO,CAAC,WAAW,CAAC,CAuC/D;AAED,wBAAsB,kBAAkB,IAAI,OAAO,CAAC,WAAW,CAAC,CA+B/D;AAkBD;;;;;GAKG;AACH,wBAAsB,qBAAqB,IAAI,OAAO,CAAC,WAAW,CAAC,CAiClE;AAED;;GAEG;AACH,wBAAsB,0BAA0B,IAAI,OAAO,CAAC,WAAW,CAAC,CA6BvE;AAED;;GAEG;AACH,wBAAsB,sBAAsB,IAAI,OAAO,CAAC,WAAW,CAAC,CAyBnE;AAED;;;;;;;;;;;;;GAaG;AACH,wBAAsB,wBAAwB,IAAI,OAAO,CAAC,WAAW,CAAC,CAWrE;AAED;;sBAEsB;AACtB,wBAAgB,uBAAuB,CAAC,GAAG,EAAE,MAAM,GAAG,MAAM,EAAE,CAiB7D;AAED,6EAA6E;AAC7E,wBAAgB,sBAAsB,CAAC,GAAG,EAAE,MAAM,GAAG,MAAM,CAM1D"}

package/dist/src/commands/doctor-project-checks.js

@@ -2,7 +2,7 @@
  * Doctor — project/monomind health checks
  * Config, memory, API keys, MCP, monograph, helpers, routing, gates, gitignore, worker metrics
  */
-import { existsSync, readFileSync, readdirSync, statSync, mkdirSync, copyFileSync, writeFileSync, appendFileSync } from 'fs';
+import { existsSync, readFileSync, readdirSync, statSync, mkdirSync, copyFileSync, writeFileSync, appendFileSync, rmSync } from 'fs';
 import { join, dirname } from 'path';
 import { fileURLToPath } from 'url';
 import { execSync } from 'child_process';
@@ -67,14 +67,42 @@ export async function checkMemoryKnowledgeGraph() {
         return { name, status: 'warn', message: `Check failed: ${err instanceof Error ? err.message : String(err)}` };
     }
 }
-/** Second Brain: when this project has an indexed knowledge base, semantic
- * search needs the local embedding model. Its absence is silent (search
- * degrades to keyword matching) — surface it here instead. */
+/** Count live (non-tombstoned) ingested documents under a brain root, without
+ * creating the directory — `listDocuments` mkdir's its metadata dir, which
+ * would materialize an empty global brain just by running doctor. */
+async function countBrainDocs(root) {
+    if (!existsSync(join(root, '.monomind', 'knowledge', 'doc-metadata.jsonl')))
+        return 0;
+    try {
+        const { listDocuments } = await import('../knowledge/document-pipeline.js');
+        return listDocuments(root).length;
+    }
+    catch {
+        return 0;
+    }
+}
+/** Second Brain: when there is any indexed knowledge — ingested docs in this
+ * project, the personal global brain, or the monograph god-node chunk —
+ * semantic search needs the local embedding model. Its absence is silent
+ * (search degrades to keyword matching), so surface it here instead. */
 export async function checkSecondBrainModel() {
     const name = 'Second Brain Model';
-    if (!existsSync(join(process.cwd(), '.monomind', 'knowledge', 'chunks.jsonl'))) {
-        return { name, status: 'pass', message: 'No knowledge base in this project (nothing to check)' };
-    }
+    const { getGlobalBrainDir, getProjectRoot } = await import('../memory/memory-bridge.js');
+    const projectDocs = await countBrainDocs(getProjectRoot());
+    const globalDocs = await countBrainDocs(getGlobalBrainDir());
+    // chunks.jsonl holds the monograph god-node chunk — knowledge with no doc
+    // ingest. Unlike the document store it is written per-CWD by the session
+    // hook, not at the project root, so check both rather than assuming.
+    const chunksIn = (root) => existsSync(join(root, '.monomind', 'knowledge', 'chunks.jsonl'));
+    const hasChunks = chunksIn(getProjectRoot()) || chunksIn(process.cwd());
+    if (!projectDocs && !globalDocs && !hasChunks) {
+        return { name, status: 'pass', message: 'No knowledge indexed (nothing to check)' };
+    }
+    const indexed = [
+        projectDocs ? `${projectDocs} project doc${projectDocs === 1 ? '' : 's'}` : null,
+        globalDocs ? `${globalDocs} global doc${globalDocs === 1 ? '' : 's'}` : null,
+        !projectDocs && !globalDocs ? 'monograph god-nodes' : null,
+    ].filter(Boolean).join(' · ');
     let entryPath = null;
     try {
         // exports map blocks package.json — resolve the entry file, then walk UP
@@ -101,7 +129,7 @@ export async function checkSecondBrainModel() {
         pkgDir = dirname(pkgDir);
     const modelCache = join(pkgDir, '.cache', 'Xenova');
     if (pkgDir.endsWith('transformers') && existsSync(modelCache)) {
-        return { name, status: 'pass', message: 'Local embedding model cached — semantic search active' };
+        return { name, status: 'pass', message: `Local embedding model cached — semantic search active (${indexed})` };
     }
     return { name, status: 'warn', message: 'Embedding model not downloaded yet — searches use keyword matching until it is', fix: 'run once while online: monomind doc search -q "warmup" (downloads ~90MB locally, one time)' };
 }
@@ -761,4 +789,79 @@ export async function checkMemoryProficiency() {
         return { name: 'Memory Proficiency', status: 'warn', message: 'Could not load intelligence module' };
     }
 }
+/** AppleDouble sidecars (`._name`) under `.claude/`.
+ *
+ * macOS writes these whenever a file carrying extended attributes is copied to
+ * a filesystem that cannot store them natively — exFAT, most USB/network
+ * volumes. Harmless as data, but Claude Code discovers skills and commands by
+ * reading `.claude/skills/` and `.claude/commands/`, and a stray
+ * `._createorg.md` is registered as a real command: a garbage entry named
+ * `mastermind:._createorg` appears in the roster, and its "content" is a binary
+ * resource fork. They also reappear after any Finder copy, `cp`, or tar
+ * extract, so a one-time delete does not hold.
+ *
+ * Reported here rather than swept silently, because deleting files under
+ * `.claude/` should be something the operator sees. `doctor --fix` removes them.
+ */
+export async function checkAppleDoubleSidecars() {
+    const name = 'AppleDouble Sidecars';
+    const found = findAppleDoubleSidecars(process.cwd());
+    if (found.length === 0)
+        return { name, status: 'pass', message: 'None under .claude/' };
+    const shown = found.slice(0, 3).map(p => p.replace(process.cwd() + '/', '')).join(', ');
+    return {
+        name,
+        status: 'warn',
+        message: `${found.length} AppleDouble file${found.length === 1 ? '' : 's'} under .claude/ (${shown}${found.length > 3 ? ', …' : ''}) — skills/commands dirs register these as real entries`,
+        fix: 'monomind doctor --fix (or: find .claude -name "._*" -type f -delete)',
+    };
+}
+/** Every `._*` file under the project's `.claude/` trees. Both the repo-root
+ *  tree and the npm-shipped copy under packages/, since a sidecar in the latter
+ *  ships to users. */
+export function findAppleDoubleSidecars(cwd) {
+    const roots = [join(cwd, '.claude'), join(cwd, 'packages', '@monomind', 'cli', '.claude')];
+    const out = [];
+    const walk = (dir, depth = 0) => {
+        if (depth > 8)
+            return;
+        let entries;
+        try {
+            entries = readdirSync(dir);
+        }
+        catch {
+            return;
+        }
+        for (const e of entries) {
+            const full = join(dir, e);
+            let isDir;
+            try {
+                isDir = statSync(full).isDirectory();
+            }
+            catch {
+                continue;
+            }
+            if (isDir)
+                walk(full, depth + 1);
+            else if (e.startsWith('._'))
+                out.push(full);
+        }
+    };
+    for (const r of roots)
+        if (existsSync(r))
+            walk(r);
+    return out;
+}
+/** Delete every AppleDouble sidecar found. Returns how many were removed. */
+export function fixAppleDoubleSidecars(cwd) {
+    let removed = 0;
+    for (const f of findAppleDoubleSidecars(cwd)) {
+        try {
+            rmSync(f, { force: true });
+            removed++;
+        }
+        catch { /* best effort */ }
+    }
+    return removed;
+}
 //# sourceMappingURL=doctor-project-checks.js.map