@pcircle/memesh 4.5.0 → 4.6.0

package/dist/transports/cli/cli.js

@@ -6,11 +6,16 @@ import path from 'path';
 import { fileURLToPath } from 'url';
 import { openDatabase, closeDatabase, getDatabase, reindexFts, allowVectorIndexRebuild } from '../../db.js';
 import { remember, recallWithConflicts, forget, exportMemories, importMemories, learn, reindex, setPinned } from '../../core/operations.js';
-import { verifyAgentWork } from '../../core/verifier.js';
 import { readConfig, writeConfig, maskApiKey, detectCapabilities } from '../../core/config.js';
 import { MAX_LANGUAGE_LENGTH, languageValueError } from '../../core/output-language.js';
-import { getDbPath } from '../../core/paths.js';
+import { getDbPath, homeDir, redactSecrets, redactUserPaths } from '../../core/paths.js';
 import { flushPendingEmbeddings, canRefillVectorIndex } from '../../core/embedder.js';
+import { NAMESPACES } from '../../core/types.js';
+import { assembleBriefing } from '../../core/briefing.js';
+import { inspectHosts, allWired } from '../../core/setup.js';
+import { installHooks } from '../../core/install-hooks.js';
+import { getTaskState, setTaskState } from '../../core/task-state-store.js';
+import { TASK_STATE_FIELDS, taskStateLines } from '../../core/task-state.js';
 async function withDatabase(fn) {
     openDatabase();
     try {
@@ -20,13 +25,40 @@ async function withDatabase(fn) {
         closeDatabase();
     }
 }
+function requireOneOf(value, allowed, flag) {
+    if (value === undefined || allowed.includes(value))
+        return;
+    console.error(`Error: ${flag} "${value}" is not valid. Use one of: ${allowed.join(', ')}.`);
+    process.exit(1);
+}
+function isOnPath(tool) {
+    const exts = process.platform === 'win32'
+        ? (process.env.PATHEXT ?? '.EXE;.CMD;.BAT;.COM').split(';').filter(Boolean)
+        : [''];
+    for (const dir of (process.env.PATH ?? '').split(path.delimiter)) {
+        if (!dir)
+            continue;
+        for (const ext of exts) {
+            try {
+                fs.accessSync(path.join(dir, tool + ext), fs.constants.X_OK);
+                return true;
+            }
+            catch { }
+        }
+    }
+    return false;
+}
+function wireUserHooks() {
+    const r = installHooks({ pluginRoot: packageRoot, pluginVersion: pkg.version, scope: 'user' });
+    return `hooks: added ${r.added}, skipped ${r.skipped} already-installed${r.backupPath ? ` (backup: ${r.backupPath})` : ''}`;
+}
 const packageJsonPath = path.resolve(path.dirname(fileURLToPath(import.meta.url)), '../../../package.json');
 const packageRoot = path.dirname(packageJsonPath);
 const pkg = JSON.parse(fs.readFileSync(packageJsonPath, 'utf8'));
 const program = new Command();
 program
     .name('memesh')
-    .description('MeMesh — Local memory for Claude Code and MCP coding agents')
+    .description('MeMesh — Agentic memory for coding agents')
     .version(pkg.version)
     .allowExcessArguments(true)
     .showSuggestionAfterError(true);
@@ -36,11 +68,15 @@ program
     .description('Store knowledge as an entity (use flags for explicit form, or positional text for quick capture)')
     .option('--name <name>', 'Entity name')
     .option('--type <type>', 'Entity type')
+    .option('--title <title>', 'Short human-readable label shown as the headline (name stays the stable machine key)')
     .option('--obs <observations...>', 'Observations (space-separated)')
     .option('--tags <tags...>', 'Tags (space-separated)')
-    .option('--namespace <namespace>', 'Namespace: personal, team, or global (default: personal)')
+    .option('--namespace <namespace>', 'Namespace: personal, team, or global. On a NEW memory this places it (default personal); on one that already exists it MOVES it out of the scope it is in — omit the flag to leave it alone.')
+    .option('--supersedes <name...>', 'This memory replaces the named one — ARCHIVES it immediately (recoverable; nothing is deleted)')
+    .option('--contradicts <name...>', 'This memory cannot both be true with the named one — both surface as a conflict on every recall')
     .option('--json', 'Output as JSON')
     .action(async (text, opts) => {
+    requireOneOf(opts.namespace, NAMESPACES, '--namespace');
     if (text && !opts.name && !opts.type) {
         const slug = String(text)
             .toLowerCase()
@@ -51,6 +87,8 @@ program
         const suffix = randomBytes(3).toString('hex');
         opts.name = `quick-${date}-${slug || 'note'}-${suffix}`;
         opts.type = 'note';
+        if (!opts.title)
+            opts.title = String(text).slice(0, 200);
         if (!opts.obs || opts.obs.length === 0)
             opts.obs = [String(text)];
         else
@@ -68,20 +106,43 @@ program
             '  memesh remember "Use OAuth 2.0 with PKCE"');
         process.exit(1);
     }
+    const relations = [
+        ...(opts.supersedes ?? []).map(to => ({ to, type: 'supersedes' })),
+        ...(opts.contradicts ?? []).map(to => ({ to, type: 'contradicts' })),
+    ];
     await withDatabase(async () => {
         const result = remember({
             name: opts.name,
             type: opts.type,
+            title: opts.title,
             observations: opts.obs,
             tags: opts.tags,
             namespace: opts.namespace,
+            relations: relations.length > 0 ? relations : undefined,
+            sourceHost: 'cli',
         });
         if (opts.json) {
             console.log(JSON.stringify(result));
         }
         else {
             console.log(`✅ Stored "${result.name}" (${result.observations} observations, ${result.tags} tags)`);
+            if (result.movedFromNamespace) {
+                console.log(`   moved: ${result.movedFromNamespace} → ${opts.namespace} (was in ${result.movedFromNamespace}; re-run with --namespace ${result.movedFromNamespace} to put it back)`);
+            }
+            if (result.superseded?.length) {
+                console.log(`   archived as superseded: ${result.superseded.join(', ')}`);
+            }
+            const contradicted = (result.relationsCreated ?? [])
+                .filter(r => r.type === 'contradicts')
+                .map(r => r.to);
+            if (contradicted.length > 0) {
+                console.log(`   conflicts stated: ${contradicted.join(', ')}`);
+            }
+            for (const err of result.relationErrors ?? [])
+                console.error(`   ⚠️  ${err}`);
         }
+        if (result.relationErrors?.length)
+            process.exitCode = 1;
         await flushPendingEmbeddings();
     });
 });
@@ -96,6 +157,7 @@ program
     .option('--cross-project', 'Search across all project tags (ignores --tag filter)')
     .option('--json', 'Output as JSON')
     .action(async (query, opts) => {
+    requireOneOf(opts.namespace, NAMESPACES, '--namespace');
     await withDatabase(async () => {
         const { entities, conflicts } = await recallWithConflicts({
             query: query || undefined,
@@ -173,8 +235,14 @@ program
         else if (result.observation_removed) {
             console.log(`✂️  Removed observation (${result.remaining_observations} remaining)`);
         }
+        else if (opts.observation && result.entity_found) {
+            console.log(`Entity "${opts.name}" has no observation matching that text (${result.remaining_observations} observation(s) present).`);
+            console.log(`See them with: memesh recall "${opts.name}" --json`);
+            process.exitCode = 1;
+        }
         else {
             console.log(`Entity "${opts.name}" not found`);
+            process.exitCode = 1;
         }
     });
 });
@@ -219,6 +287,31 @@ program
     console.error('so it is not a like-for-like replacement for compressing one named entity.');
     process.exitCode = 1;
 });
+program
+    .command('verify')
+    .description('(retired) Removed with the agentic-orchestration experiment — see the message this prints')
+    .allowUnknownOption()
+    .action(() => {
+    console.error('`memesh verify` has been retired, along with the agentic-orchestration experiment.');
+    console.error('');
+    console.error('It recorded a verification report for background-agent work. The protocol it');
+    console.error('served was removed without ever leaving opt-in. Run your own verification');
+    console.error('(typecheck / tests / lint) and store conclusions with `memesh remember` if you');
+    console.error('want them remembered. Existing verification_record entities are untouched.');
+    process.exitCode = 1;
+});
+program
+    .command('patterns')
+    .description('(retired) Removed with the agentic-orchestration experiment — see the message this prints')
+    .allowUnknownOption()
+    .action(() => {
+    console.error('`memesh patterns` has been retired, along with the agentic-orchestration experiment.');
+    console.error('');
+    console.error('It displayed the experiment\'s local skill-usage telemetry, which is no longer');
+    console.error('written. A leftover ~/.memesh/skill-usage.jsonl is inert and safe to delete.');
+    console.error('For work-pattern insights, use the `user_patterns` MCP tool or GET /v1/patterns.');
+    process.exitCode = 1;
+});
 program
     .command('export')
     .description('Export memories as JSON. Defaults to stdout (pipe-friendly); use `-o <file>` to write directly.')
@@ -227,6 +320,7 @@ program
     .option('--limit <n>', 'Max entities to export', '1000')
     .option('-o, --out <file>', 'Write JSON to <file> instead of stdout. Parent directory must exist.')
     .action(async (opts) => {
+    requireOneOf(opts.namespace, NAMESPACES, '--namespace');
     await withDatabase(() => {
         const result = exportMemories({
             tag: opts.tag,
@@ -235,6 +329,12 @@ program
         });
         const json = JSON.stringify(result, null, 2);
         if (opts.out) {
+            const outDir = path.dirname(path.resolve(opts.out));
+            if (!fs.existsSync(outDir)) {
+                console.error(`Error: cannot write ${opts.out} — the directory ${outDir} does not exist.`);
+                console.error(`       Create it first (mkdir -p "${outDir}"), or drop -o to write to stdout.`);
+                process.exit(1);
+            }
             fs.writeFileSync(opts.out, json + '\n');
             process.stderr.write(`✅ Exported ${result.entity_count} entities to ${opts.out}\n`);
         }
@@ -250,6 +350,8 @@ program
     .option('--namespace <ns>', 'Override namespace for all imported entities')
     .option('--merge <strategy>', 'Merge strategy: skip | overwrite | append', 'skip')
     .action(async (file, opts) => {
+    requireOneOf(opts.merge, ['skip', 'overwrite', 'append'], '--merge');
+    requireOneOf(opts.namespace, NAMESPACES, '--namespace');
     await withDatabase(() => {
         let raw;
         try {
@@ -281,11 +383,18 @@ program
             console.error(`       Try: memesh export > my-export.json && memesh import my-export.json`);
             process.exit(1);
         }
-        const result = importMemories({
-            data: data,
-            namespace: opts.namespace,
-            merge_strategy: opts.merge,
-        });
+        let result;
+        try {
+            result = importMemories({
+                data: data,
+                namespace: opts.namespace,
+                merge_strategy: opts.merge,
+            });
+        }
+        catch (err) {
+            console.error(`Error: ${err instanceof Error ? err.message : String(err)}`);
+            process.exit(1);
+        }
         console.log(`Imported: ${result.imported}, Skipped: ${result.skipped}, Appended: ${result.appended}`);
         if (result.errors.length > 0) {
             console.error(`Errors:\n  ${result.errors.join('\n  ')}`);
@@ -303,6 +412,7 @@ program
     .option('--severity <level>', 'Severity: critical|major|minor', 'minor')
     .option('--json', 'Output as JSON')
     .action(async (opts) => {
+    requireOneOf(opts.severity, ['critical', 'major', 'minor'], '--severity');
     await withDatabase(() => {
         const result = learn({
             error: opts.error,
@@ -310,6 +420,7 @@ program
             root_cause: opts.rootCause,
             prevention: opts.prevention,
             severity: opts.severity,
+            sourceHost: 'cli',
         });
         if (opts.json) {
             console.log(JSON.stringify(result));
@@ -320,47 +431,162 @@ program
     });
 });
 program
-    .command('verify <workdir>')
-    .description('Record a verification report for agent work in <workdir>. ' +
-    'Exit codes: 0 pass, 1 fail, 2 unverified (nothing was checked).')
-    .requiredOption('--agent-id <id>', 'Identifier for the agent being verified')
-    .option('--base <ref>', 'Git ref to diff against (default: merge-base with origin/main)')
-    .option('--expected-files <n>', 'Number of files the agent claimed to change', (v) => parseInt(v, 10))
-    .option('--report <path>', 'Path to a JSON file with pre-computed report (typecheck/tests/lint/build)')
+    .command('briefing')
+    .description('The assembled work topology for a project — task state, decisions, lessons, knowledge, recent activity')
+    .option('--project <name>', 'Project name (default: the current directory’s project)')
     .option('--json', 'Output as JSON')
-    .action(async (workdir, opts) => {
+    .action(async (opts) => {
     await withDatabase(() => {
-        let externalReport;
-        let result;
+        const result = assembleBriefing(opts.project);
+        if (opts.json) {
+            console.log(JSON.stringify(result));
+            return;
+        }
+        if (!result.text) {
+            console.log(`No memories for "${result.project}" yet.\n` +
+                `Capture happens automatically as you work; or set the task state:  memesh task --goal "…"`);
+            return;
+        }
+        console.log(result.text);
+    });
+});
+program
+    .command('setup')
+    .description('Detect Claude Code / Codex / Gemini on this machine, wire memesh into each, and verify')
+    .option('--check', 'Only report wiring status per host; change nothing (exit 1 if a present host is unwired)')
+    .option('--yes', 'Apply every wiring action without asking')
+    .action(async (opts) => {
+    const { spawnSync, execFileSync } = await import('child_process');
+    const runSeam = (cmd, args) => {
         try {
-            if (opts.report) {
-                const raw = fs.readFileSync(opts.report, 'utf8');
-                externalReport = JSON.parse(raw);
+            let target = cmd;
+            let useShell = false;
+            if (process.platform === 'win32') {
+                const resolved = execFileSync('where', [cmd], { encoding: 'utf8' }).split(/\r?\n/)[0]?.trim();
+                if (resolved) {
+                    target = resolved;
+                    useShell = /\.(cmd|bat)$/i.test(resolved);
+                }
             }
-            result = verifyAgentWork({
-                agent_id: opts.agentId,
-                workdir: path.resolve(workdir),
-                base: opts.base,
-                claim: opts.expectedFiles != null ? { expected_files: opts.expectedFiles } : undefined,
-                report: externalReport,
-            });
+            const r = spawnSync(target, args, { encoding: 'utf8', shell: useShell });
+            return { status: r.status, stderr: r.stderr ?? '' };
         }
         catch (err) {
-            console.error(err instanceof Error ? err.message : String(err));
-            console.error('Nothing was checked (exit 2 = unverified).');
-            process.exit(2);
+            return { status: null, stderr: err instanceof Error ? err.message : String(err) };
+        }
+    };
+    const seams = { home: () => homeDir(), isOnPath, run: runSeam };
+    const render = (statuses) => {
+        for (const st of statuses) {
+            if (!st.present) {
+                console.log(`   ${st.title}: not found (looked for ${st.presenceDetail}) — skipped`);
+                continue;
+            }
+            const mark = st.wired === true ? '✅' : st.wired === false ? '❌' : '❓';
+            console.log(`${mark} ${st.title}: ${st.wiredDetail}`);
+        }
+    };
+    let statuses = inspectHosts(seams);
+    if (opts.check) {
+        render(statuses);
+        process.exit(allWired(statuses) ? 0 : 1);
+    }
+    const pending = statuses.filter((st) => st.present && st.actions.length > 0);
+    if (pending.length === 0) {
+        render(statuses);
+        console.log(allWired(statuses)
+            ? '\nEverything present is wired. Nothing to do.'
+            : '\nNothing to wire automatically — see the lines above.');
+        process.exit(allWired(statuses) ? 0 : 1);
+    }
+    render(statuses);
+    console.log('\nPlanned actions:');
+    for (const st of pending)
+        for (const a of st.actions) {
+            console.log(`  • [${st.title}] ${a.label}${a.cmd ? `\n      ${a.cmd} ${(a.args ?? []).join(' ')}` : ''}`);
+        }
+    if (!opts.yes && !process.stdin.isTTY) {
+        console.error('\nNot a terminal and --yes not given — nothing was changed. Re-run with: memesh setup --yes');
+        process.exit(1);
+    }
+    const confirmAll = Boolean(opts.yes);
+    let rl = null;
+    if (!confirmAll) {
+        const { createInterface } = await import('node:readline/promises');
+        rl = createInterface({ input: process.stdin, output: process.stdout });
+    }
+    let failed = false;
+    for (const st of pending) {
+        for (const action of st.actions) {
+            if (!confirmAll && rl) {
+                const answer = (await rl.question(`\n[${st.title}] ${action.label} — proceed? [y/N] `)).trim().toLowerCase();
+                if (answer !== 'y' && answer !== 'yes') {
+                    console.log('  skipped');
+                    continue;
+                }
+            }
+            if (action.kind === 'install-hooks') {
+                console.log(`  ✅ ${wireUserHooks()}`);
+            }
+            else if (action.cmd) {
+                const r = runSeam(action.cmd, action.args ?? []);
+                if (r.status === 0)
+                    console.log(`  ✅ done (${action.cmd} ${(action.args ?? []).join(' ')})`);
+                else {
+                    console.error(`  ❌ ${action.cmd} exited ${r.status ?? 'without running'}${r.stderr ? `: ${r.stderr.trim()}` : ''}`);
+                    failed = true;
+                }
+            }
         }
-        if (opts.json) {
-            console.log(JSON.stringify(result, null, 2));
+    }
+    rl?.close();
+    console.log('\nAfter wiring:');
+    statuses = inspectHosts(seams);
+    render(statuses);
+    process.exit(failed || !allWired(statuses) ? 1 : 0);
+});
+program
+    .command('task')
+    .description('Show or update where the work stands on this project')
+    .option('--project <name>', 'Project name (default: the current directory’s project)')
+    .option('--goal <text>', 'What this work is FOR — the outcome being aimed at')
+    .option('--next <text>', 'The next concrete step')
+    .option('--blocked <text>', 'What is standing in the way (pass "" to clear it once resolved)')
+    .option('--done <text>', 'What was just finished')
+    .option('--json', 'Output as JSON')
+    .action(async (opts) => {
+    await withDatabase(() => {
+        const patch = {};
+        for (const field of TASK_STATE_FIELDS) {
+            if (opts[field] !== undefined)
+                patch[field] = opts[field];
         }
-        else {
-            console.log(`${result.verdict.toUpperCase()}  agent=${opts.agentId}  entity=${result.entity_name}`);
-            console.log(`  reality: ${result.reality_check.summary}`);
-            if (result.verdict === 'unverified') {
-                console.log('  nothing was checked — pass --expected-files <n> and/or --report <file> to verify something.');
+        if (Object.keys(patch).length === 0) {
+            const { project, state } = getTaskState(opts.project);
+            if (opts.json) {
+                console.log(JSON.stringify({ project, state }));
+                return;
             }
+            const lines = taskStateLines(state, project);
+            if (lines.length === 0) {
+                console.log(`Nothing recorded for "${project}" yet.\n` +
+                    `Set it with:  memesh task --goal "…" --next "…"`);
+                return;
+            }
+            console.log(lines.join('\n'));
+            return;
+        }
+        const result = setTaskState({ project: opts.project, patch, sourceHost: 'cli' });
+        if (opts.json) {
+            console.log(JSON.stringify(result));
+            return;
         }
-        process.exit(result.verdict === 'pass' ? 0 : result.verdict === 'fail' ? 1 : 2);
+        if (result.changed.length === 0) {
+            console.log(`No change — "${result.project}" already said exactly that.`);
+            return;
+        }
+        console.log(`Updated ${result.changed.join(', ')} for "${result.project}".`);
+        console.log(taskStateLines(result.state, result.project).join('\n'));
     });
 });
 const configCmd = program.command('config').description('Manage configuration');
@@ -392,10 +618,10 @@ const ALLOWED_KEYS = new Set([
     'embedder.model',
     'autoUpdate',
     'sessionLimit',
-    'enableAgenticOrchestration',
     'autoCapture',
     'llmFallbacks',
     'language',
+    'transcriptMining',
 ]);
 const KEY_VALIDATORS = {
     'llm.provider': (v) => ['anthropic', 'openai', 'ollama'].includes(v) ? null : `must be one of: anthropic, openai, ollama`,
@@ -462,7 +688,7 @@ function formatConfigValue(key, raw) {
         return JSON.stringify(raw);
     return String(raw);
 }
-export function buildConfigListing(config) {
+function buildConfigListing(config) {
     const rows = [];
     for (const key of Array.from(ALLOWED_KEYS).sort()) {
         const raw = getNested(config, key.split('.'));
@@ -516,7 +742,10 @@ configCmd
         coerced = parseInt(value, 10);
     if (canonical === 'llmFallbacks')
         coerced = JSON.parse(value);
-    if (canonical === 'enableAgenticOrchestration' || canonical === 'autoCapture') {
+    if (canonical === 'autoCapture') {
+        coerced = value === 'true' || value === '1';
+    }
+    if (canonical === 'transcriptMining') {
         coerced = value === 'true' || value === '1';
     }
     const config = readConfig();
@@ -524,6 +753,10 @@ configCmd
     writeConfig(config);
     const displayValue = canonical.toLowerCase().includes('key') ? maskApiKey(String(value)) : String(value);
     console.log(`✅ Set ${canonical} = ${displayValue}`);
+    if (canonical === 'llm.apiKey' && !config.llm?.provider) {
+        console.log('⚠️  No llm.provider is set, so this key is not used yet and LLM features stay off.');
+        console.log('    Set one with: memesh config set llm.provider <anthropic|openai|ollama>');
+    }
 });
 configCmd
     .command('unset')
@@ -592,10 +825,16 @@ program
     .description('Start the HTTP API server and web dashboard')
     .option('--port <port>', 'Port number', '3737')
     .option('--host <host>', 'Host to bind', '127.0.0.1')
-    .option('--allow-remote', 'Allow binding to non-loopback hosts. A bearer token is generated and REQUIRED for every /v1 request — the startup output shows where it lives and how to rotate it.')
+    .option('--allow-remote', 'Permit binding to a non-loopback host. Pair it with --host; on a non-loopback bind a bearer token is generated and REQUIRED for every /v1 request, and the startup output says where it lives. On the default loopback host this flag changes nothing.')
     .action(async (opts) => {
     const { startServer } = await import('../http/server.js');
-    startServer(opts.host, parseInt(opts.port, 10), { allowRemote: opts.allowRemote, autoUpdateCheck: true });
+    try {
+        startServer(opts.host, parseInt(opts.port, 10), { allowRemote: opts.allowRemote, autoUpdateCheck: true });
+    }
+    catch (err) {
+        console.error(`MeMesh: ${err instanceof Error ? err.message : String(err)}`);
+        process.exit(1);
+    }
 });
 program
     .command('update')
@@ -634,6 +873,53 @@ program
         process.exit(1);
     }
 });
+program
+    .command('upgrade-plugin')
+    .description('Upgrade the Claude Code plugin install (finds and runs its bundled upgrade script)')
+    .action(async () => {
+    const { spawnSync } = await import('child_process');
+    const cacheRoot = path.join(homeDir(), '.claude', 'plugins', 'cache', 'pcircle-memesh', 'memesh');
+    let versions = [];
+    try {
+        versions = fs.readdirSync(cacheRoot, { withFileTypes: true })
+            .filter((entry) => entry.isDirectory() && /^\d+\.\d+\.\d+/.test(entry.name))
+            .map((entry) => entry.name);
+    }
+    catch { }
+    if (versions.length === 0) {
+        console.error('No Claude Code plugin install found (looked in ~/.claude/plugins/cache/pcircle-memesh).');
+        console.error('If you installed via npm, upgrade with: memesh update');
+        process.exit(1);
+    }
+    versions.sort((a, b) => a.localeCompare(b, undefined, { numeric: true }));
+    const newest = versions[versions.length - 1];
+    const script = path.join(cacheRoot, newest, 'scripts', 'upgrade-plugin.sh');
+    if (!fs.existsSync(script)) {
+        console.error(`Plugin install found (v${newest}), but it has no scripts/upgrade-plugin.sh — plugin versions before 4.2.5 shipped without it.`);
+        console.error('Reinstall once from the Claude Code /plugin UI, or run the npm-global copy directly:');
+        console.error('  bash "$(npm prefix -g)/lib/node_modules/@pcircle/memesh/scripts/upgrade-plugin.sh"');
+        process.exit(1);
+    }
+    const installHints = {
+        node: 'node is required by the upgrade script. Install Node.js from https://nodejs.org',
+        npm: 'npm is required by the upgrade script. It ships with Node.js — reinstall from https://nodejs.org',
+        rsync: 'rsync is required by the upgrade script. macOS: already installed; Debian/Ubuntu: sudo apt install rsync',
+    };
+    const missing = Object.keys(installHints).filter((tool) => !isOnPath(tool));
+    if (missing.length > 0) {
+        for (const tool of missing)
+            console.error(installHints[tool]);
+        process.exit(1);
+    }
+    const run = spawnSync('bash', [script], { stdio: 'inherit' });
+    if (run.error) {
+        console.error(`Could not run the upgrade script: ${run.error.message}`);
+        console.error('bash is required to run it. If bash is available under another name, run it yourself:');
+        console.error(`  bash ${script}`);
+        process.exit(1);
+    }
+    process.exit(run.status ?? 1);
+});
 program
     .command('telemetry')
     .description('Show LLM call telemetry (per-flow scorecard for the last N days)')
@@ -641,6 +927,12 @@ program
     .option('--prune <days>', 'Delete rows older than N days BEFORE rendering (closes v4.2.0 retention gap)', (v) => parseInt(v, 10))
     .option('--json', 'Output as JSON')
     .action(async (opts) => {
+    for (const [flag, value] of [['--window', opts.window], ['--prune', opts.prune]]) {
+        if (value !== undefined && !Number.isFinite(value)) {
+            console.error(`Error: ${flag} needs a number of days.`);
+            process.exit(1);
+        }
+    }
     await withDatabase(async () => {
         const { summariseTelemetry, pruneTelemetry } = await import('../../core/llm-telemetry.js');
         let pruneResult = null;
@@ -856,15 +1148,82 @@ program
     .option('--probe-http', 'Also probe the local HTTP server health endpoint')
     .option('--probe', 'Make one small live call to the configured LLM to confirm it actually answers')
     .option('--url <url>', 'Base URL for --probe-http', 'http://127.0.0.1:3737')
+    .option('--fix', 'Apply the whitelisted fixes doctor prescribes (asks per fix; --yes skips asking)')
+    .option('--yes', 'With --fix: apply without asking')
     .action(async (opts) => {
     const { formatDoctorReport, runDoctor } = await import('../../core/doctor.js');
-    const result = await runDoctor({
+    let result = await runDoctor({
         packageRoot,
         packageVersion: pkg.version,
         probeHttp: opts.probeHttp,
         probeCapabilities: opts.probe,
         httpBaseUrl: opts.url,
     });
+    if (opts.fix) {
+        const FIX_ACTIONS = {
+            'install-hooks': wireUserHooks,
+            'fts-rebuild': () => {
+                openDatabase();
+                try {
+                    return `keyword index rebuilt (${reindexFts().entities} entities)`;
+                }
+                finally {
+                    closeDatabase();
+                }
+            },
+            'chmod-db': () => {
+                fs.chmodSync(getDbPath(), 0o600);
+                return `permissions restored: chmod 600 ${getDbPath()}`;
+            },
+        };
+        const fixable = result.checks.filter((c) => c.fixId && (c.status === 'warn' || c.status === 'fail'));
+        if (fixable.length === 0) {
+            console.log('Nothing on the --fix whitelist to apply.');
+        }
+        else {
+            if (!opts.yes && !process.stdin.isTTY) {
+                console.error('Not a terminal and --yes not given — nothing was changed. Re-run with: memesh doctor --fix --yes');
+                process.exit(1);
+            }
+            let rl = null;
+            if (!opts.yes) {
+                const { createInterface } = await import('node:readline/promises');
+                rl = createInterface({ input: process.stdin, output: process.stdout });
+            }
+            for (const check of fixable) {
+                console.log(`\n${check.label}: ${check.summary}`);
+                if (rl) {
+                    const answer = (await rl.question(`Apply fix (${check.fixId})? [y/N] `)).trim().toLowerCase();
+                    if (answer !== 'y' && answer !== 'yes') {
+                        console.log('  skipped');
+                        continue;
+                    }
+                }
+                try {
+                    console.log(`  ✅ ${FIX_ACTIONS[check.fixId]()}`);
+                }
+                catch (err) {
+                    console.error(`  ❌ ${err instanceof Error ? err.message : String(err)}`);
+                }
+            }
+            rl?.close();
+            console.log('\nAfter fixes:');
+            const before = new Map(result.checks.map((c) => [c.id, c.status]));
+            const fixedIds = new Set(fixable.map((c) => c.id));
+            result = await runDoctor({
+                packageRoot,
+                packageVersion: pkg.version,
+                probeHttp: false,
+                probeCapabilities: false,
+                httpBaseUrl: opts.url,
+            });
+            for (const c of result.checks) {
+                const was = before.get(c.id);
+                if (fixedIds.has(c.id) && was && was !== c.status)
+                    console.log(`  ${c.label}: ${was} → ${c.status}`);
+            }
+        }
+    }
     if (opts.json) {
         console.log(JSON.stringify(result, null, 2));
     }
@@ -1011,6 +1370,11 @@ dreamCmd
         });
         console.log(`${opts.dryRun ? '[dry-run] ' : ''}Dream pass complete in ${result.durationMs}ms`);
         console.log(`  clusters scanned: ${result.clustersScanned}`);
+        if (result.clusteringMode) {
+            console.log(`  grouped by:       ${result.clusteringMode === 'semantic' ? 'meaning (embeddings)' : 'calendar week (no embeddings)'}`);
+        }
+        if (result.clusteringNote)
+            console.log(`    note: ${result.clusteringNote}`);
         console.log(`  LLM calls:        ${result.llmCalls}`);
         console.log(`  proposals created: ${result.proposalsCreated}`);
         if (result.skipped.length > 0) {
@@ -1094,7 +1458,8 @@ dreamCmd
         console.log(`${proposals.length} ${opts.status} proposal(s):`);
         console.log('');
         for (const p of proposals) {
-            const srcLabel = p.source_kind === 'transcript' ? ' (transcript)' : '';
+            const srcLabel = p.kind === 'relation' ? ' (conflict)'
+                : p.source_kind === 'transcript' ? ' (transcript)' : '';
             console.log(`  #${p.id}  [${p.project}/${p.cluster_key}]${srcLabel}  ${p.source_count} source(s) → "${p.digest_name}"`);
             if (p.digest_observations_preview !== null) {
                 console.log(`         ${p.digest_observations_preview}`);
@@ -1105,6 +1470,49 @@ dreamCmd
         console.log(`Inspect: memesh dream show <id>   |   Apply: memesh dream accept <id>   |   Reject: memesh dream reject <id>`);
     });
 });
+dreamCmd
+    .command('conflicts')
+    .description('Judge semantically-close memory pairs for contradiction / supersession / duplication (LLM) and stage relation proposals for review')
+    .option('--max-pairs <n>', 'Judge at most N of the tightest candidate pairs this run (default 20)', (v) => parseInt(v, 10))
+    .option('--dry-run', 'Show how many candidates are queued without calling an LLM or writing anything')
+    .action(async (opts) => {
+    await withDatabase(async () => {
+        const cfg = readConfig();
+        const llm = detectCapabilities().llm;
+        if (!llm) {
+            console.error('No LLM configured. Run `memesh config set llm.provider <anthropic|openai|ollama>` first (or set ANTHROPIC_API_KEY / OPENAI_API_KEY).');
+            console.error('LLM is required for `memesh dream conflicts` because "do these two entries disagree" is a semantic judgement, not a rule.');
+            process.exit(1);
+        }
+        const { judgeConflicts, CONFLICT_JUDGE_MAX_PAIRS } = await import('../../core/conflict-judge.js');
+        const { getDatabase } = await import('../../db.js');
+        const result = await judgeConflicts(getDatabase(), llm, {
+            maxPairs: typeof opts.maxPairs === 'number' && !Number.isNaN(opts.maxPairs) ? opts.maxPairs : CONFLICT_JUDGE_MAX_PAIRS,
+            dryRun: !!opts.dryRun,
+            fallbacks: cfg.llmFallbacks,
+        });
+        console.log(`${opts.dryRun ? '[dry-run] ' : ''}Conflict pass complete in ${result.durationMs}ms`);
+        console.log(`  candidate pairs available: ${result.candidatesAvailable}`);
+        if (opts.dryRun) {
+            console.log('  (dry run — no LLM called, nothing judged or written)');
+            return;
+        }
+        console.log(`  LLM calls:      ${result.llmCalls}`);
+        console.log(`  judged:         ${result.judged} (${result.unrelated} unrelated, remembered so they are never re-bought)`);
+        console.log(`  staged:         ${result.staged} relation proposal(s)`);
+        if (result.llmFailures > 0) {
+            console.log(`  failed:         ${result.llmFailures} (unparseable or errored LLM responses; those pairs stay at the head of the candidate list and are retried next run)`);
+        }
+        if (result.aborted) {
+            console.error(`  ABORTED after the work above: ${result.aborted}`);
+            process.exit(1);
+        }
+        if (result.staged > 0) {
+            console.log('');
+            console.log('Review: memesh dream list   |   Apply: memesh dream accept <id>   |   Reject: memesh dream reject <id>');
+        }
+    });
+});
 dreamCmd
     .command('show <id>')
     .description('Show a proposal in full — name, type, ALL observations, tags, source — so you can review the whole thing before accepting')
@@ -1126,6 +1534,31 @@ dreamCmd
         console.log(`Proposal #${detail.id}  [${detail.project}/${detail.cluster_key}]  source: ${detail.source_kind}  status: ${detail.status}`);
         console.log(`created: ${detail.created_at}`);
         console.log('');
+        if (detail.kind === 'relation') {
+            const rel = detail.relation;
+            if (!rel) {
+                console.error('relation payload is corrupt — reject this proposal');
+                process.exit(1);
+            }
+            const [fromE, toE] = rel.relation_type === 'supersedes' && rel.direction === 'b_supersedes_a' ? [rel.b, rel.a] : [rel.a, rel.b];
+            console.log(`verdict: ${rel.verdict}  (severity: ${rel.severity ?? 'unknown'})`);
+            console.log(`accepting creates: ${fromE?.name} —${rel.relation_type}→ ${toE?.name}`);
+            if (rel.relation_type === 'supersedes') {
+                console.log(`  survivor: ${fromE?.name}  (the arrow points from the surviving claim to the obsolete one)`);
+            }
+            console.log(`rationale: ${rel.rationale ?? '(none given)'}`);
+            if (rel.recommended_action)
+                console.log(`recommended action: ${rel.recommended_action}`);
+            if (rel.excerpts?.a || rel.excerpts?.b) {
+                console.log(`excerpt A (${rel.a?.name}): ${rel.excerpts?.a ?? ''}`);
+                console.log(`excerpt B (${rel.b?.name}): ${rel.excerpts?.b ?? ''}`);
+            }
+            if (typeof rel.cosine_distance === 'number')
+                console.log(`cosine distance: ${rel.cosine_distance.toFixed(3)}`);
+            console.log('');
+            console.log(`Accept: memesh dream accept ${detail.id}   |   Reject: memesh dream reject ${detail.id}`);
+            return;
+        }
         console.log(`name: ${detail.digest.name}`);
         console.log(`type: ${detail.digest.type}`);
         console.log(`observations (${detail.digest.observations.length}):`);
@@ -1209,6 +1642,9 @@ program
         }
         console.log(`${opts.dryRun ? '[dry-run] ' : ''}Settings: ${result.settingsPath}`);
         console.log(`${opts.dryRun ? '[dry-run] Would add ' : 'Added '}${result.added} hook entr${result.added === 1 ? 'y' : 'ies'}, ${opts.dryRun ? 'would skip ' : 'skipped '}${result.skipped} already-installed.`);
+        if (result.pruned > 0) {
+            console.log(`${opts.dryRun ? '[dry-run] Would remove ' : 'Removed '}${result.pruned} retired memesh hook entr${result.pruned === 1 ? 'y' : 'ies'} no longer shipped by this version.`);
+        }
         if (result.backupPath)
             console.log(`Backup: ${result.backupPath}`);
         if (result.conflicts.length > 0) {
@@ -1289,11 +1725,19 @@ program
             body += `\n\n---\n**System Info**\n- Version: \`${pkg.version}\`\n- Node: \`${process.version}\`\n- Platform: \`${process.platform} ${process.arch}\`\n_Diagnostics unavailable: doctor probe failed._`;
         }
     }
-    const url = `https://github.com/PCIRCLE-AI/memesh-llm-memory/issues/new?title=${encodeURIComponent(`[${typeLabel}] `)}&body=${encodeURIComponent(body)}&labels=${encodeURIComponent(labels)}`;
+    body = redactUserPaths(redactSecrets(body));
+    const url = `https://github.com/PCIRCLE-AI/memesh/issues/new?title=${encodeURIComponent(`[${typeLabel}] `)}&body=${encodeURIComponent(body)}&labels=${encodeURIComponent(labels)}`;
     if (opts.open === false) {
         console.log(url);
         return;
     }
+    console.log('This will be pre-filled into a PUBLIC GitHub issue:');
+    console.log('---');
+    console.log(body);
+    console.log('---');
+    if (opts.diagnostics !== false) {
+        console.log('Re-run with --no-diagnostics to leave out the install ID and the doctor report.');
+    }
     const { spawn } = await import('child_process');
     const cmd = process.platform === 'darwin' ? 'open'
         : process.platform === 'win32' ? 'cmd'
@@ -1319,6 +1763,7 @@ program
     'stored embedding first. Needed only when switching embedding providers.')
     .option('--json', 'Output as JSON')
     .action(async (opts) => {
+    requireOneOf(opts.namespace, NAMESPACES, '--namespace');
     try {
         if (opts.fts) {
             if (opts.vectors) {
@@ -1403,33 +1848,6 @@ program
         throw err;
     }
 });
-program
-    .command('patterns')
-    .description('Show local skill-usage telemetry (agentic-orchestration banner injections, verify_agent_work invocations). Local-only — never uploaded.')
-    .option('--json', 'Output as JSON')
-    .action(async (opts) => {
-    const { summariseSkillUsage } = await import('../../core/skill-usage-log.js');
-    const summary = summariseSkillUsage();
-    if (opts.json) {
-        console.log(JSON.stringify(summary, null, 2));
-        return;
-    }
-    console.log(`Skill usage log: ${summary.log_path}`);
-    console.log(`  total events: ${summary.total_events}`);
-    console.log(`  log size:     ${summary.log_bytes} bytes`);
-    if (summary.first_event)
-        console.log(`  first event:  ${summary.first_event}`);
-    if (summary.last_event)
-        console.log(`  last event:   ${summary.last_event}`);
-    if (summary.total_events === 0) {
-        console.log('  (no events recorded yet — open a Claude Code session with memesh installed, or run a verification, to start collecting)');
-        return;
-    }
-    console.log('  events by name:');
-    for (const [name, count] of Object.entries(summary.events_by_name).sort((a, b) => b[1] - a[1])) {
-        console.log(`    ${count.toString().padStart(6)}  ${name}`);
-    }
-});
 program
     .command('status')
     .description('Show MeMesh status and capabilities')
@@ -1444,7 +1862,7 @@ program
     console.log(`MeMesh v${pkg.version}`);
     console.log(`Search level: ${caps.searchLevel} (${caps.searchLevel === 1 ? 'Smart Mode' : 'Core'})`);
     console.log(`Embeddings: ${caps.embeddings}`);
-    console.log(`LLM: ${caps.llm ? `${caps.llm.provider} (${caps.llm.model})` : 'not configured'}`);
+    console.log(`LLM: ${caps.llm ? `${caps.llm.provider} (${caps.llm.model ?? 'default'})` : 'not configured'}`);
     console.log(`Install method: ${installSupport.label}`);
     for (const line of formatUpdateCheckStatus(update)) {
         console.log(`\n${line}`);