@monoes/monomindcli 1.18.6 → 1.18.7

package/dist/src/commands/doc.js

@@ -0,0 +1,183 @@
+/**
+ * CLI Document Command — Second Brain document management
+ */
+import * as path from 'node:path';
+import { output } from '../output.js';
+const ingestCommand = {
+    name: 'ingest',
+    description: 'Ingest documents into the knowledge base',
+    options: [
+        { name: 'scope', short: 's', description: 'Knowledge scope (default: shared)', type: 'string', default: 'shared' },
+    ],
+    examples: [
+        { command: 'monomind doc ingest ./docs', description: 'Ingest all docs in a directory' },
+        { command: 'monomind doc ingest report.pdf', description: 'Ingest a single file' },
+    ],
+    action: async (ctx) => {
+        const target = ctx.args[0] || '.';
+        const scope = String(ctx.flags.scope || 'shared');
+        const { ingestDocument, ingestDirectory } = await import('../knowledge/document-pipeline.js');
+        const fs = await import('node:fs');
+        const resolved = path.resolve(target);
+        const spinner = output.createSpinner({ text: 'Indexing documents...' });
+        spinner.start();
+        try {
+            const stat = fs.statSync(resolved);
+            if (stat.isDirectory()) {
+                const result = await ingestDirectory(resolved, scope, {
+                    rootDir: ctx.cwd || process.cwd(),
+                    onProgress: (file, done, total) => {
+                        spinner.setText(`[${done + 1}/${total}] ${path.basename(file)}`);
+                    },
+                });
+                spinner.succeed(`Indexed ${result.totalChunks} chunks from ${result.filesProcessed} files (${result.filesSkipped} skipped)`);
+                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 };
+            }
+            else {
+                const result = await ingestDocument(resolved, scope);
+                if (result.skipped && !result.error) {
+                    spinner.succeed(`Already indexed: ${path.basename(resolved)} (${result.chunksIndexed} chunks)`);
+                }
+                else if (result.error) {
+                    spinner.fail(result.error);
+                    return { success: false };
+                }
+                else {
+                    spinner.succeed(`Indexed ${result.chunksIndexed} chunks from ${path.basename(resolved)}`);
+                }
+                return { success: true, data: result };
+            }
+        }
+        catch (err) {
+            spinner.fail(String(err));
+            return { success: false, exitCode: 1 };
+        }
+    },
+};
+const searchDocCommand = {
+    name: 'search',
+    description: 'Semantic search over indexed documents',
+    options: [
+        { name: 'query', short: 'q', description: 'Search query', type: 'string', required: true },
+        { name: 'limit', short: 'l', description: 'Max results (default: 10)', type: 'number', default: 10 },
+        { name: 'scope', short: 's', description: 'Knowledge scope (default: shared)', type: 'string', default: 'shared' },
+        { name: 'min-score', description: 'Minimum similarity (default: 0.3)', type: 'number', default: 0.3 },
+    ],
+    examples: [
+        { command: 'monomind doc search -q "authentication flow"', description: 'Search for auth docs' },
+    ],
+    action: async (ctx) => {
+        const query = String(ctx.flags.query || ctx.args[0] || '');
+        if (!query) {
+            output.printError('Query required: monomind doc search -q "your query"');
+            return { success: false, exitCode: 1 };
+        }
+        const { searchKnowledge } = await import('../knowledge/document-pipeline.js');
+        const excerpts = await searchKnowledge(query, {
+            scope: String(ctx.flags.scope || 'shared'),
+            limit: Number(ctx.flags.limit || 10),
+            minScore: Number(ctx.flags['min-score'] || 0.3),
+        });
+        if (!excerpts.length) {
+            output.writeln(output.dim('No results found.'));
+            return { success: true, data: [] };
+        }
+        output.writeln(output.bold(`${excerpts.length} results:`));
+        output.writeln();
+        for (let i = 0; i < excerpts.length; i++) {
+            const ex = excerpts[i];
+            output.writeln(`${output.highlight(`${i + 1}.`)} ${output.dim(`(${ex.similarity.toFixed(3)})`)} ${ex.filePath || 'unknown'}`);
+            const preview = ex.text.length > 200 ? ex.text.slice(0, 200) + '...' : ex.text;
+            output.writeln(`   ${output.dim(preview)}`);
+            output.writeln();
+        }
+        return { success: true, data: excerpts };
+    },
+};
+const listDocCommand = {
+    name: 'list',
+    description: 'List indexed documents',
+    options: [
+        { name: 'scope', short: 's', description: 'Knowledge scope', type: 'string' },
+    ],
+    action: async (ctx) => {
+        const { listDocuments } = await import('../knowledge/document-pipeline.js');
+        const scope = ctx.flags.scope ? String(ctx.flags.scope) : undefined;
+        const docs = listDocuments(process.cwd(), scope);
+        if (!docs.length) {
+            output.writeln(output.dim('No documents indexed. Run: monomind doc ingest <path>'));
+            return { success: true, data: [] };
+        }
+        output.writeln(output.bold(`${docs.length} documents indexed:`));
+        output.writeln();
+        for (const doc of docs) {
+            const name = path.basename(doc.filePath);
+            const size = doc.size > 1024 * 1024
+                ? `${(doc.size / 1024 / 1024).toFixed(1)}MB`
+                : `${(doc.size / 1024).toFixed(0)}KB`;
+            const date = doc.indexedAt.slice(0, 10);
+            output.writeln(`  ${output.highlight(name)} ${output.dim(`${doc.chunkCount} chunks · ${size} · ${date} · ${doc.scope}`)}`);
+        }
+        return { success: true, data: docs };
+    },
+};
+const exportDocCommand = {
+    name: 'export',
+    description: 'Export knowledge base as OKF bundle (markdown + frontmatter)',
+    options: [
+        { name: 'output', short: 'o', description: 'Output directory', type: 'string', default: '.monomind/knowledge-export' },
+        { name: 'scope', short: 's', description: 'Knowledge scope (default: shared)', type: 'string', default: 'shared' },
+    ],
+    action: async (ctx) => {
+        const { exportToOKF } = await import('../knowledge/document-pipeline.js');
+        const outDir = path.resolve(String(ctx.flags.output || '.monomind/knowledge-export'));
+        const scope = String(ctx.flags.scope || 'shared');
+        const spinner = output.createSpinner({ text: 'Exporting to OKF...' });
+        spinner.start();
+        try {
+            const result = await exportToOKF(outDir, process.cwd(), scope);
+            spinner.succeed(`Exported ${result.exported} documents to ${result.outputDir}`);
+            return { success: true, data: result };
+        }
+        catch (err) {
+            spinner.fail(String(err));
+            return { success: false, exitCode: 1 };
+        }
+    },
+};
+export const docCommand = {
+    name: 'doc',
+    description: 'Second Brain — document knowledge management',
+    aliases: ['docs', 'knowledge'],
+    subcommands: [ingestCommand, searchDocCommand, listDocCommand, exportDocCommand],
+    options: [],
+    examples: [
+        { command: 'monomind doc ingest ./docs', description: 'Index documents' },
+        { command: 'monomind doc search -q "auth flow"', description: 'Semantic search' },
+        { command: 'monomind doc list', description: 'List indexed docs' },
+        { command: 'monomind doc export', description: 'Export as OKF bundle' },
+    ],
+    action: async () => {
+        output.writeln();
+        output.writeln(output.bold('Second Brain — Document Knowledge Management'));
+        output.writeln();
+        output.writeln('Usage: monomind doc <subcommand> [options]');
+        output.writeln();
+        output.writeln('Subcommands:');
+        output.printList([
+            `${output.highlight('ingest')}  - Ingest documents into the knowledge base`,
+            `${output.highlight('search')}  - Semantic search over indexed documents`,
+            `${output.highlight('list')}    - List indexed documents`,
+            `${output.highlight('export')}  - Export as OKF bundle (markdown + frontmatter)`,
+        ]);
+        return { success: true };
+    },
+};
+export default docCommand;
+//# sourceMappingURL=doc.js.map

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

@@ -0,0 +1 @@
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package/dist/src/commands/doctor-monoes-checks.d.ts

@@ -0,0 +1,12 @@
+/**
+ * Doctor — monoes tool family checks (monotask, mono-agent, mono-clip)
+ *
+ * Opt-in component only (`monomind doctor -c monoes-tools`) — not part of the
+ * always-on check set, since these are unrelated sibling tools on this machine,
+ * not monomind dependencies. Catches known Homebrew tap-rename and Gatekeeper
+ * issues discovered while installing them via /monoes:install.
+ */
+import type { HealthCheck } from './doctor-env-checks.js';
+export declare function checkMonoesTools(): Promise<HealthCheck>;
+export declare function fixMonoesTools(): Promise<boolean>;
+//# sourceMappingURL=doctor-monoes-checks.d.ts.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"doctor-monoes-checks.d.ts","sourceRoot":"","sources":["../../../src/commands/doctor-monoes-checks.ts"],"names":[],"mappings":"AAAA;;;;;;;GAOG;AAMH,OAAO,KAAK,EAAE,WAAW,EAAE,MAAM,wBAAwB,CAAC;AAoH1D,wBAAsB,gBAAgB,IAAI,OAAO,CAAC,WAAW,CAAC,CAe7D;AAED,wBAAsB,cAAc,IAAI,OAAO,CAAC,OAAO,CAAC,CAyBvD"}

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

@@ -0,0 +1,160 @@
+/**
+ * Doctor — monoes tool family checks (monotask, mono-agent, mono-clip)
+ *
+ * Opt-in component only (`monomind doctor -c monoes-tools`) — not part of the
+ * always-on check set, since these are unrelated sibling tools on this machine,
+ * not monomind dependencies. Catches known Homebrew tap-rename and Gatekeeper
+ * issues discovered while installing them via /monoes:install.
+ */
+import { existsSync } from 'fs';
+import { execSync } from 'child_process';
+import { output } from '../output.js';
+import { runCommand } from './doctor-env-checks.js';
+async function commandExists(cmd) {
+    try {
+        await runCommand(`command -v ${cmd}`);
+        return true;
+    }
+    catch {
+        return false;
+    }
+}
+async function findMonoesIssues() {
+    const issues = [];
+    // 1. Tap rename ambiguity: nokhodian/tap was renamed to monoes/tap. Having both
+    //    tapped makes formula/cask lookups ambiguous ("found in multiple taps").
+    try {
+        const taps = await runCommand('brew tap');
+        const hasOld = /(^|\n)nokhodian\/tap(\n|$)/.test(taps);
+        const hasNew = /(^|\n)monoes\/tap(\n|$)/.test(taps);
+        if (hasOld && hasNew) {
+            // --force is safe here: brew refuses a plain untap because it sees formula/cask
+            // names matching this tap's checkout, even when they're actually installed from
+            // monoes/tap (same upstream repo, redirected). Verified against INSTALL_RECEIPT.json
+            // before relying on this — the receipts point at monoes/tap, not this one.
+            issues.push({
+                message: 'both nokhodian/tap and monoes/tap are tapped — formula/cask lookups are ambiguous',
+                fixCommand: 'brew untap --force nokhodian/tap',
+            });
+        }
+        else if (hasOld && !hasNew) {
+            issues.push({
+                message: 'nokhodian/tap is tapped but was renamed to monoes/tap',
+                fixCommand: 'brew untap --force nokhodian/tap && brew tap monoes/tap',
+            });
+        }
+    }
+    catch {
+        // brew not usable for tap listing — skip this sub-check
+    }
+    // 2. monotask formula installed but not linked as `monotask` on PATH. Homebrew
+    //    ships the raw binary as `monotaskcli` and skips auto-linking when the
+    //    same-named `monotask` cask is also installed.
+    try {
+        const cellarRoot = await runCommand('brew --cellar');
+        if (cellarRoot && existsSync(`${cellarRoot}/monotask`) && !(await commandExists('monotask'))) {
+            issues.push({
+                message: "monotask formula is installed but 'monotask' isn't on PATH (Homebrew installs it as 'monotaskcli' and skips linking when the same-named cask is present)",
+                fixCommand: 'ln -sf "$(brew --cellar)"/monotask/*/bin/monotaskcli "$(brew --prefix)/bin/monotask"',
+            });
+        }
+    }
+    catch {
+        // skip
+    }
+    // 3. MonoClip.app quarantined/unsigned — macOS can silently move it to Trash on
+    //    its first launch instead of showing the "damaged" dialog.
+    try {
+        if (existsSync('/Applications/MonoClip.app')) {
+            let quarantined = true;
+            try {
+                await runCommand('xattr -p com.apple.quarantine "/Applications/MonoClip.app"');
+            }
+            catch {
+                quarantined = false;
+            }
+            if (quarantined) {
+                issues.push({
+                    message: 'MonoClip.app is quarantined — macOS may silently move it to Trash on first launch',
+                    fixCommand: 'find /Applications/MonoClip.app -print0 | xargs -0 xattr -c && codesign --force --deep --sign - /Applications/MonoClip.app',
+                });
+            }
+        }
+    }
+    catch {
+        // skip
+    }
+    // 4. mono-agent (monoagentcli) — distributed as a raw GitHub release binary, not
+    //    through Homebrew, so it never gets picked up by `brew upgrade`. Check it
+    //    against the latest GitHub release directly.
+    try {
+        if (await commandExists('monoagentcli')) {
+            const versionOut = await runCommand('monoagentcli version');
+            const m = versionOut.match(/v?(\d+\.\d+\.\d+)/);
+            if (m) {
+                const current = m[1];
+                try {
+                    const releaseJson = await runCommand('curl -fsSL https://api.github.com/repos/monoes/mono-agent/releases/latest', 8000);
+                    const latestTag = (JSON.parse(releaseJson).tag_name || '').replace(/^v/, '');
+                    if (latestTag && latestTag !== current) {
+                        issues.push({
+                            message: `monoagentcli is v${current}, latest release is v${latestTag}`,
+                            fixCommand: 'ARCH=$(uname -m); [ "$ARCH" = "x86_64" ] && ARCH=amd64; ' +
+                                'curl -fsSL --max-time 30 "https://github.com/monoes/mono-agent/releases/latest/download/monoagentcli-darwin-${ARCH}" -o /tmp/monoagentcli && ' +
+                                'chmod +x /tmp/monoagentcli && sudo mv /tmp/monoagentcli /usr/local/bin/monoagentcli',
+                        });
+                    }
+                }
+                catch {
+                    // GitHub API unreachable/rate-limited — skip version-freshness sub-check
+                }
+            }
+        }
+    }
+    catch {
+        // skip
+    }
+    return issues;
+}
+export async function checkMonoesTools() {
+    if (process.platform !== 'darwin') {
+        return { name: 'monoes Tools', status: 'pass', message: 'Skipped (macOS-only — monotask/mono-agent/mono-clip are macOS tools)' };
+    }
+    const issues = await findMonoesIssues();
+    if (issues.length === 0) {
+        return { name: 'monoes Tools', status: 'pass', message: 'No known monotask/mono-agent/mono-clip install issues detected' };
+    }
+    return {
+        name: 'monoes Tools',
+        status: 'warn',
+        message: issues.map(i => i.message).join('; '),
+        fix: issues.map(i => i.fixCommand).join('  |  '),
+    };
+}
+export async function fixMonoesTools() {
+    output.writeln();
+    output.writeln(output.bold('Applying monoes tools fixes...'));
+    const issues = await findMonoesIssues();
+    if (issues.length === 0) {
+        output.writeln(output.dim('Nothing to fix.'));
+        return true;
+    }
+    let allOk = true;
+    for (const issue of issues) {
+        try {
+            // 2min timeout: generous enough for an interactive sudo password prompt
+            // (mono-agent's fix uses sudo mv), but still bounded — avoids hanging the
+            // whole `doctor --install` run on a stalled brew/curl network call.
+            execSync(issue.fixCommand, { encoding: 'utf8', stdio: 'inherit', shell: '/bin/bash', timeout: 120_000 });
+            output.writeln(output.success(`Fixed: ${issue.message}`));
+        }
+        catch (error) {
+            allOk = false;
+            output.writeln(output.warning(`Fix failed for: ${issue.message}`));
+            if (error instanceof Error)
+                output.writeln(output.dim(error.message));
+        }
+    }
+    return allOk;
+}
+//# sourceMappingURL=doctor-monoes-checks.js.map

package/dist/src/commands/doctor-monoes-checks.js.map

@@ -0,0 +1 @@
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package/dist/src/commands/doctor-project-checks.d.ts

@@ -17,4 +17,8 @@ export declare function checkMonoesIntegration(): Promise<HealthCheck>;
 export declare function checkGitignoreCoverage(): Promise<HealthCheck>;
 export declare function checkAgentRegistry(): Promise<HealthCheck>;
 export declare function checkGuidanceGates(): Promise<HealthCheck>;
+/**
+ * AutoMem proficiency check — reports memory learning health (arXiv:2607.01224)
+ */
+export declare function checkMemoryProficiency(): Promise<HealthCheck>;
 //# sourceMappingURL=doctor-project-checks.d.ts.map

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

@@ -1 +1 @@
-{"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,iBAAiB,IAAI,OAAO,CAAC,WAAW,CAAC,CAgB9D;AAED,wBAAsB,mBAAmB,IAAI,OAAO,CAAC,WAAW,CAAC,CAahE;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;AA4CD,wBAAsB,iBAAiB,IAAI,OAAO,CAAC,WAAW,CAAC,CAa9D;AAqBD,wBAAsB,sBAAsB,IAAI,OAAO,CAAC,WAAW,CAAC,CAMnE;AAmBD,wBAAsB,sBAAsB,IAAI,OAAO,CAAC,WAAW,CAAC,CAmBnE;AAED,wBAAsB,kBAAkB,IAAI,OAAO,CAAC,WAAW,CAAC,CAuC/D;AAED,wBAAsB,kBAAkB,IAAI,OAAO,CAAC,WAAW,CAAC,CAwB/D"}
+{"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,iBAAiB,IAAI,OAAO,CAAC,WAAW,CAAC,CAgB9D;AAED,wBAAsB,mBAAmB,IAAI,OAAO,CAAC,WAAW,CAAC,CAahE;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;AA4CD,wBAAsB,iBAAiB,IAAI,OAAO,CAAC,WAAW,CAAC,CAa9D;AAqBD,wBAAsB,sBAAsB,IAAI,OAAO,CAAC,WAAW,CAAC,CAMnE;AAmBD,wBAAsB,sBAAsB,IAAI,OAAO,CAAC,WAAW,CAAC,CAmBnE;AAED,wBAAsB,kBAAkB,IAAI,OAAO,CAAC,WAAW,CAAC,CAuC/D;AAED,wBAAsB,kBAAkB,IAAI,OAAO,CAAC,WAAW,CAAC,CAwB/D;AAED;;GAEG;AACH,wBAAsB,sBAAsB,IAAI,OAAO,CAAC,WAAW,CAAC,CA0BnE"}

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

@@ -429,4 +429,32 @@ export async function checkGuidanceGates() {
         return { name: 'Guidance Gates', status: 'warn', message: 'Could not parse .claude/settings.json', fix: 'monomind guidance setup --force' };
     }
 }
+/**
+ * AutoMem proficiency check — reports memory learning health (arXiv:2607.01224)
+ */
+export async function checkMemoryProficiency() {
+    try {
+        const intelligenceMod = await import('../memory/intelligence.js');
+        const stats = intelligenceMod.getMemoryProficiencyStats();
+        const bankStats = intelligenceMod.getIntelligenceStats();
+        if (stats.totalDecisions === 0) {
+            return {
+                name: 'Memory Proficiency',
+                status: 'warn',
+                message: 'No memory decisions recorded yet — AutoMem LOG/PLAN not active',
+                fix: 'Complete tasks with pre-task/post-task hooks enabled',
+            };
+        }
+        const successPct = Math.round(stats.successRate * 100);
+        const hitPct = Math.round(stats.patternHitRate * 100);
+        const msg = `${stats.totalDecisions} decisions, ${successPct}% success, ${stats.proficiencyPatterns} patterns, ${hitPct}% hit rate (bank: ${bankStats.patternsLearned} total)`;
+        if (stats.successRate < 0.5) {
+            return { name: 'Memory Proficiency', status: 'warn', message: msg };
+        }
+        return { name: 'Memory Proficiency', status: 'pass', message: msg };
+    }
+    catch {
+        return { name: 'Memory Proficiency', status: 'warn', message: 'Could not load intelligence module' };
+    }
+}
 //# sourceMappingURL=doctor-project-checks.js.map

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

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

@@ -1 +1 @@
-{"version":3,"file":"doctor.d.ts","sourceRoot":"","sources":["../../../src/commands/doctor.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAGH,OAAO,KAAK,EAAE,OAAO,EAAiC,MAAM,aAAa,CAAC;AAsB1E,eAAO,MAAM,aAAa,EAAE,OA4J3B,CAAC;AAEF,eAAe,aAAa,CAAC"}
+{"version":3,"file":"doctor.d.ts","sourceRoot":"","sources":["../../../src/commands/doctor.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAGH,OAAO,KAAK,EAAE,OAAO,EAAiC,MAAM,aAAa,CAAC;AAuB1E,eAAO,MAAM,aAAa,EAAE,OA6K3B,CAAC;AAEF,eAAe,aAAa,CAAC"}

package/dist/src/commands/doctor.js

@@ -7,7 +7,8 @@
 import * as path from 'path';
 import { output } from '../output.js';
 import { checkNodeVersion, checkNpmVersion, checkGit, checkGitRepo, checkDiskSpace, checkBuildTools, checkVersionFreshness, checkClaudeCode, installClaudeCode, } from './doctor-env-checks.js';
-import { checkConfigFile, checkDaemonStatus, checkMemoryDatabase, checkApiKeys, checkMcpServers, checkMonograph, checkMonographFreshness, checkMonoesMemory, checkHelpersFresh, checkMonoesIntegration, checkGuidanceGates, checkGitignoreCoverage, checkAgentRegistry, } from './doctor-project-checks.js';
+import { checkConfigFile, checkDaemonStatus, checkMemoryDatabase, checkApiKeys, checkMcpServers, checkMonograph, checkMonographFreshness, checkMonoesMemory, checkHelpersFresh, checkMonoesIntegration, checkGuidanceGates, checkGitignoreCoverage, checkAgentRegistry, checkMemoryProficiency, } from './doctor-project-checks.js';
+import { checkMonoesTools, fixMonoesTools } from './doctor-monoes-checks.js';
 function formatCheck(check) {
     const icon = check.status === 'pass' ? output.success('✓') :
         check.status === 'warn' ? output.warning('⚠') :
@@ -22,7 +23,7 @@ export const doctorCommand = {
         { name: 'install', short: 'i', description: 'Auto-install missing dependencies (Claude Code CLI)', type: 'boolean', default: false },
         {
             name: 'component', short: 'c',
-            description: 'Check specific component (version, node, npm, config, daemon, memory, api, git, mcp, claude, disk, typescript, monograph, graph-freshness, memory-pkg, helpers, monoes, gates, gitignore, registry)',
+            description: 'Check specific component (version, node, npm, config, daemon, memory, api, git, mcp, claude, disk, typescript, monograph, graph-freshness, memory-pkg, helpers, monoes, gates, gitignore, registry, monoes-tools)',
             type: 'string',
         },
         { name: 'verbose', short: 'v', description: 'Verbose output', type: 'boolean', default: false },
@@ -33,6 +34,7 @@ export const doctorCommand = {
         { command: 'monomind doctor --install', description: 'Auto-install missing dependencies' },
         { command: 'monomind doctor -c version', description: 'Check for stale npx cache' },
         { command: 'monomind doctor -c claude', description: 'Check Claude Code CLI only' },
+        { command: 'monomind doctor -c monoes-tools --install', description: 'Check/fix monotask, mono-agent, mono-clip install issues (opt-in, not in the default run)' },
     ],
     action: async (ctx) => {
         const showFix = ctx.flags.fix;
@@ -62,6 +64,7 @@ export const doctorCommand = {
             checkConfigFile, checkMemoryDatabase, checkDiskSpace,
             checkMonograph, checkMonoesMemory, checkHelpersFresh, checkMonoesIntegration,
             checkGuidanceGates, checkAgentRegistry, checkGit, checkDaemonStatus, checkApiKeys,
+            checkMemoryProficiency,
         ];
         const codeOnlyChecks = [
             checkGitRepo, checkMcpServers,
@@ -79,7 +82,8 @@ export const doctorCommand = {
             'graph-freshness': checkMonographFreshness, 'memory-pkg': checkMonoesMemory,
             helpers: checkHelpersFresh, monoes: checkMonoesIntegration,
             gates: checkGuidanceGates, gitignore: checkGitignoreCoverage,
-            registry: checkAgentRegistry,
+            registry: checkAgentRegistry, 'memory-proficiency': checkMemoryProficiency,
+            'monoes-tools': checkMonoesTools,
         };
         const checksToRun = (component && componentMap[component]) ? [componentMap[component]] : allChecks;
         const results = [];
@@ -127,6 +131,20 @@ export const doctorCommand = {
                     output.writeln(formatCheck(newCheck));
                 }
             }
+            const monoesToolsResult = results.find(r => r.name === 'monoes Tools');
+            if (monoesToolsResult && monoesToolsResult.status !== 'pass') {
+                if (await fixMonoesTools()) {
+                    const newCheck = await checkMonoesTools();
+                    const idx = results.findIndex(r => r.name === 'monoes Tools');
+                    if (idx !== -1) {
+                        results[idx] = newCheck;
+                        const fixIdx = fixes.findIndex(f => f.startsWith('monoes Tools:'));
+                        if (fixIdx !== -1 && newCheck.status === 'pass')
+                            fixes.splice(fixIdx, 1);
+                    }
+                    output.writeln(formatCheck(newCheck));
+                }
+            }
         }
         const passed = results.filter(r => r.status === 'pass').length;
         const warnings = results.filter(r => r.status === 'warn').length;