claude-recall 0.26.1 → 0.27.1

package/.claude/hooks/search_enforcer.py

@@ -36,8 +36,13 @@ PASSTHROUGH_TOOLS = [
     'AskUserQuestion',                        # User interaction
 ]
 
-# Read-only bash commands that don't need memory search
-READ_ONLY_BASH = [
+# Bash command prefixes exempt from the load-rules gate. NOT all read-only:
+# alongside inspection commands, routine dev-workflow commands (git commit,
+# npm test, ...) are deliberately exempt — the gate exists to get rules loaded
+# before Claude starts shaping code, and blocking mid-workflow git/npm calls
+# adds friction without a safety benefit. This is an advisory nudge, not a
+# security boundary.
+EXEMPT_BASH_PREFIXES = [
     'ls', 'cat', 'head', 'tail', 'less', 'more', 'file', 'stat', 'wc',
     'find', 'locate', 'which', 'whereis', 'type', 'pwd', 'whoami',
     'git status', 'git log', 'git diff', 'git show', 'git branch',
@@ -67,7 +72,7 @@ def load_state(session_id: str) -> dict:
     if state_file.exists():
         try:
             return json.load(open(state_file))
-        except:
+        except Exception:
             pass
     return {'lastSearchAt': None, 'searchQuery': None}
 
@@ -76,7 +81,7 @@ def save_state(session_id: str, state: dict):
     STATE_DIR.mkdir(parents=True, exist_ok=True)
     try:
         json.dump(state, open(get_state_file(session_id), 'w'), indent=2)
-    except:
+    except Exception:
         pass
 
 
@@ -84,18 +89,26 @@ def is_search_tool(tool_name: str) -> bool:
     return any(s in tool_name for s in SEARCH_TOOLS)
 
 
-def is_read_only_bash(command: str) -> bool:
+def _has_command_prefix(cmd: str, prefix: str) -> bool:
+    """Word-boundary prefix match: 'cat foo' matches 'cat', but
+    'catastrophic-script.sh' and 'envsubst' do not match 'cat'/'env'."""
+    if not cmd.startswith(prefix):
+        return False
+    rest = cmd[len(prefix):]
+    return rest == '' or rest[0] in ' \t;|&'
+
+
+def is_exempt_bash(command: str) -> bool:
     if not command:
         return False
     cmd = command.strip().lower()
-    # Check direct match or pipe starting with read-only
-    for ro in READ_ONLY_BASH:
-        if cmd.startswith(ro):
-            return True
+    # Check direct match, or the first segment of a pipeline
+    candidates = [cmd]
     if '|' in cmd:
-        first = cmd.split('|')[0].strip()
-        for ro in READ_ONLY_BASH:
-            if first.startswith(ro):
+        candidates.append(cmd.split('|')[0].strip())
+    for candidate in candidates:
+        for prefix in EXEMPT_BASH_PREFIXES:
+            if _has_command_prefix(candidate, prefix):
                 return True
     return False
 
@@ -106,7 +119,7 @@ def main():
 
     try:
         data = json.load(sys.stdin)
-    except:
+    except Exception:
         sys.exit(0)
 
     tool_name = data.get('tool_name', '')
@@ -139,14 +152,20 @@ def main():
     if not last_search:
         if tool_name not in ENFORCE_TOOLS:
             sys.exit(0)
-        # Mutation tool on first call — fall through to blocking logic below.
+        # Exempt bash passes even before rules are loaded — previously this
+        # exemption only existed on the post-load branch, so the very first
+        # `git status`/`ls` of a session was hard-blocked up to MAX_BLOCKS
+        # times, contradicting the "read-only exploration passes freely" rule.
+        if tool_name == 'Bash' and is_exempt_bash(tool_input.get('command', '')):
+            sys.exit(0)
+        # Other mutation tool on first call — fall through to blocking logic below.
     else:
         # Rules loaded at least once — only enforce on mutation tools
         if tool_name not in ENFORCE_TOOLS:
             sys.exit(0)
 
-        # Skip read-only bash
-        if tool_name == 'Bash' and is_read_only_bash(tool_input.get('command', '')):
+        # Skip exempt bash
+        if tool_name == 'Bash' and is_exempt_bash(tool_input.get('command', '')):
             sys.exit(0)
 
     if last_search:

package/.claude/skills/memory-management/SKILL.md

@@ -131,9 +131,9 @@ memories to form a skill (3+ for most types, 5+ for preferences). If so, it writ
 a SKILL.md file that Claude Code loads automatically.
 
 **CLI commands:**
-- `npx claude-recall skills list` — see generated skills
-- `npx claude-recall skills generate --force` — force regeneration
-- `npx claude-recall skills clean --force` — remove all auto-generated skills
+- `claude-recall skills list` — see generated skills
+- `claude-recall skills generate --force` — force regeneration
+- `claude-recall skills clean --force` — remove all auto-generated skills
 
 ## Automatic Capture Hooks
 
@@ -158,7 +158,7 @@ Claude Recall registers hooks on six Claude Code events for automatic capture, j
 - Auto-checkpoint quality gate: refuses to save when the LLM detects the task was already complete — manual checkpoints stay sticky
 - Always exits 0 — hooks never block Claude
 
-**Setup:** Run `npx claude-recall setup --install` to register hooks in `.claude/settings.json`. After any upgrade, re-run `setup --install` in each project so newly-added hook events get registered (claude-recall uses a `hooksVersion` field to signal when registration has changed).
+**Setup:** Run `claude-recall setup --install` to register hooks in `.claude/settings.json`. After an upgrade whose release notes mention new or changed hooks (a `hooksVersion` bump), re-run it in each active project — it's idempotent, so when hooks are already current it's a no-op and touches nothing.
 
 ## Example Workflows
 

package/README.md

@@ -49,6 +49,16 @@ claude mcp add claude-recall -- claude-recall mcp start
 
 Restart Claude Code. Ask *"Load my rules"* to verify — Claude should call `load_rules`.
 
+Prefer it active in **every** project? Register the MCP server once at user scope instead of per project (memories stay isolated per project either way — scoping comes from the working directory, not the install):
+
+```bash
+claude mcp add --scope user claude-recall -- claude-recall mcp start
+```
+
+Hook-based auto-capture remains a per-project opt-in via `claude-recall setup --install` (it writes to that project's `.claude/settings.json`).
+
+> **Do NOT add claude-recall as a project dependency** (`npm install claude-recall` inside a project). All projects share one database at `~/.claude-recall/` and whatever binary touches it runs schema migrations — multiple project-local copies at different versions fight over the same file. Worse, `npx claude-recall` prefers a project-local copy over your up-to-date global one, so a stale local install silently shadows every upgrade. One global binary; per-project *activation* only.
+
 > **Hit `EACCES: permission denied`?** Your global npm is owned by root. Either `sudo npm install -g claude-recall` once, or do the permanent fix described in [Upgrading](#upgrading) below.
 
 ### Install for Pi
@@ -71,6 +81,15 @@ claude-recall upgrade
 
 One command. Checks the registry, refreshes the global binary, clears any running MCP servers — Claude Code respawns them on the next tool call, picking up the new version. **No `claude mcp add` re-run needed** — existing registrations point at the `claude-recall` command, not a pinned path.
 
+If the release notes mention new or changed hooks (a `hooksVersion` bump), also re-run `claude-recall setup --install` in each active project. It's safe to run any time: when your hooks are already current it's a no-op and touches nothing.
+
+> **Registered before v0.27.x?** Older versions auto-registered the MCP server with an `npx`-based command, which re-resolves the package on every server start and can be shadowed by stale project-local installs. Switch to the direct binary form (run in each affected project):
+>
+> ```bash
+> claude mcp remove claude-recall
+> claude mcp add claude-recall -- claude-recall mcp start
+> ```
+
 For Pi, run `pi update npm:claude-recall` and restart Pi.
 
 > **Seeing `error: unknown command 'upgrade'`?** Your installed version predates 0.23.2 (the release that added the `upgrade` command). Bootstrap once with `npm install -g claude-recall@latest`, then all future upgrades use `claude-recall upgrade`.

package/dist/cli/claude-recall-cli.js

@@ -49,6 +49,11 @@ const mcp_commands_1 = require("./commands/mcp-commands");
 const project_commands_1 = require("./commands/project-commands");
 const hook_commands_1 = require("./commands/hook-commands");
 const repair_1 = require("./commands/repair");
+// v14 = add PreToolUse rule-injector + Post resolver for JITRI.
+// Bump when the hook block template changes — setup skips the settings
+// rewrite when the installed hooksVersion already matches.
+const HOOKS_VERSION = '14.0.0';
+const parse_utils_1 = require("./parse-utils");
 const program = new commander_1.Command();
 class ClaudeRecallCLI {
     constructor(options) {
@@ -232,7 +237,7 @@ class ClaudeRecallCLI {
         // Sort by timestamp (newest first)
         failures.sort((a, b) => (b.timestamp || 0) - (a.timestamp || 0));
         // Limit results
-        const limit = options.limit || 10;
+        const limit = (0, parse_utils_1.parsePositiveInt)(options.limit, 'limit', 10);
         const displayFailures = failures.slice(0, limit);
         console.log('\n❌ Failure Memories (Counterfactual Learning)\n');
         console.log(`Found ${failures.length} failures (showing ${displayFailures.length})\n`);
@@ -241,9 +246,20 @@ class ClaudeRecallCLI {
             return;
         }
         displayFailures.forEach((failure, index) => {
-            const value = typeof failure.value === 'string'
-                ? JSON.parse(failure.value)
-                : failure.value;
+            // One malformed row must not crash the whole listing — fall back to the
+            // raw string as content
+            let value;
+            if (typeof failure.value === 'string') {
+                try {
+                    value = JSON.parse(failure.value);
+                }
+                catch {
+                    value = { content: failure.value };
+                }
+            }
+            else {
+                value = failure.value;
+            }
             const content = value.content || value;
             console.log(`${index + 1}. ${value.title || 'Untitled Failure'}`);
             console.log(`   What Failed: ${content.what_failed || 'Unknown'}`);
@@ -394,10 +410,21 @@ class ClaudeRecallCLI {
         const needsInstall = current !== latest;
         if (needsInstall) {
             console.log(`\n📦 Upgrading ${current} → ${latest}...\n`);
-            // Run npm install -g, streaming output so the user sees progress / errors live
+            // Run npm install -g, streaming output so the user sees progress / errors live.
+            // shell: true on Windows — npm is npm.cmd there and a bare spawnSync ENOENTs.
             const install = spawnSync('npm', ['install', '-g', 'claude-recall@latest'], {
                 stdio: 'inherit',
+                shell: process.platform === 'win32',
             });
+            if (install.error && install.error.code === 'ENOENT') {
+                // spawn failed before npm ever ran — the EACCES advice below would be
+                // misleading here (previous behavior: status === null !== 0 fell
+                // through to the "sudo npm install" remediation for a missing npm)
+                console.error('\n❌ npm not found on PATH.');
+                console.error('\nInstall Node.js (which includes npm) ≥ 20.19, or fix your PATH, then re-run:');
+                console.error('  claude-recall upgrade');
+                process.exit(1);
+            }
             if (install.status !== 0) {
                 // npm prints its own error — add the practical remediation on top
                 console.error('\n❌ Install failed.');
@@ -534,7 +561,7 @@ class ClaudeRecallCLI {
      * Show outcome-aware learning status: episodes, outcome events, candidate lessons, memory stats
      */
     showOutcomes(options) {
-        const limit = options.limit || 10;
+        const limit = (0, parse_utils_1.parsePositiveInt)(options.limit, 'limit', 10);
         const section = options.section;
         const db = this.memoryService.getDatabase();
         // Check if outcome tables exist
@@ -619,7 +646,7 @@ class ClaudeRecallCLI {
      * Search memories by query
      */
     search(query, options) {
-        const limit = options.limit || 10;
+        const limit = (0, parse_utils_1.parsePositiveInt)(options.limit, 'limit', 10);
         // Determine search scope
         let results;
         if (options.global) {
@@ -709,7 +736,7 @@ class ClaudeRecallCLI {
     /**
      * Import memories from a file
      */
-    async import(inputPath) {
+    async import(inputPath, options = {}) {
         try {
             if (!fs.existsSync(inputPath)) {
                 console.error(`❌ File not found: ${inputPath}`);
@@ -724,11 +751,19 @@ class ClaudeRecallCLI {
             let imported = 0;
             for (const memory of data.memories) {
                 try {
+                    // Preserve each memory's original scoping. Exported rows carry
+                    // project_id/scope as columns (not inside context) — the previous
+                    // `context: memory.context || {}` dropped them, silently rescoping
+                    // every imported memory to the CURRENT project. --project overrides.
                     this.memoryService.store({
                         key: memory.key || `imported_${Date.now()}_${Math.random()}`,
                         value: memory.value,
                         type: memory.type || 'imported',
-                        context: memory.context || {}
+                        context: {
+                            ...(memory.context || {}),
+                            projectId: options.project ?? memory.project_id ?? memory.context?.projectId,
+                            scope: memory.scope ?? memory.context?.scope ?? null,
+                        }
                     });
                     imported++;
                 }
@@ -736,8 +771,8 @@ class ClaudeRecallCLI {
                     console.warn(`⚠️  Failed to import memory: ${error}`);
                 }
             }
-            console.log(`✅ Imported ${imported}/${data.memories.length} memories`);
-            this.logger.info('CLI', 'Import completed', { imported, total: data.memories.length });
+            console.log(`✅ Imported ${imported}/${data.memories.length} memories${options.project ? ` (rescoped to project: ${options.project})` : ' (original project scoping preserved)'}`);
+            this.logger.info('CLI', 'Import completed', { imported, total: data.memories.length, project: options.project });
         }
         catch (error) {
             console.error('❌ Import failed:', error);
@@ -908,7 +943,7 @@ class ClaudeRecallCLI {
         else if (!hasPi) {
             console.log('Claude Code MCP:');
             console.log('  Status: Not registered');
-            console.log('  Command: claude mcp add claude-recall claude-recall mcp start');
+            console.log('  Command: claude mcp add claude-recall -- claude-recall mcp start');
         }
         else {
             // Pi is present; show Claude Code MCP as optional
@@ -948,7 +983,7 @@ class ClaudeRecallCLI {
     async store(content, options) {
         try {
             const type = options.type || 'preference';
-            const confidence = options.confidence || 0.8;
+            const confidence = (0, parse_utils_1.parseUnitFloat)(options.confidence, 'confidence', 0.8);
             // Parse metadata if provided
             let metadata = {};
             if (options.metadata) {
@@ -1034,8 +1069,7 @@ async function main() {
         }
     }
     // Install skills + minimal enforcement hook
-    // TODO: honor force — currently `repair --reinstall-hooks` behaves identically to `setup --install`
-    function installSkillsAndHook(_force = false) {
+    function installSkillsAndHook(force = false) {
         const cwd = process.cwd();
         const projectName = path.basename(cwd);
         console.log('\n📦 Claude Recall Setup\n');
@@ -1103,6 +1137,18 @@ async function main() {
             catch (e) {
                 settings = {};
             }
+            // Idempotent re-run: hook block already at the current version → leave
+            // settings.json untouched (no rewrite, no backup churn) but still
+            // refresh skills below. `force` (repair --reinstall-hooks) rewrites
+            // unconditionally — the recovery path for a corrupted or hand-edited
+            // block. Previously force was accepted and ignored, so the two
+            // commands behaved identically.
+            if (!force && settings.hooksVersion === HOOKS_VERSION) {
+                console.log(`✅ Hooks already at v${HOOKS_VERSION} — settings.json untouched (use \`repair --reinstall-hooks\` to force a rewrite)`);
+                installSkills(claudeDir, packageSkillsDir);
+                console.log('\n✅ Setup complete!\n');
+                return;
+            }
             const existingHooks = settings.hooks;
             const hasExistingHooks = existingHooks
                 && typeof existingHooks === 'object'
@@ -1116,11 +1162,18 @@ async function main() {
                 console.log('   from other tools that need to coexist.');
             }
         }
-        // Resolve the CLI script path so hooks use the local install instead of npx.
-        // This avoids registry lookups on every hook invocation.
+        // Prefer the portable `claude-recall` form when the binary is on PATH —
+        // absolute dist paths break on every nvm switch or prefix move, the exact
+        // failure class `repair` exists to fix (repair already treats the PATH
+        // form as canonical). Absolute path only as fallback.
+        const onPath = (0, repair_1.resolveOnPath)('claude-recall');
         const cliScript = path.join(packageDir, 'dist', 'cli', 'claude-recall-cli.js');
-        const hookCmd = `node ${cliScript} hook run`;
-        settings.hooksVersion = '14.0.0'; // v14 = add PreToolUse rule-injector + Post resolver for JITRI
+        const hookCmd = onPath ? 'claude-recall hook run' : `node ${cliScript} hook run`;
+        if (!onPath) {
+            console.log('⚠️  claude-recall not on PATH — hooks will use an absolute path (breaks if the install moves).');
+            console.log('   `npm install -g claude-recall` gives move-proof hooks; `claude-recall repair` can convert later.');
+        }
+        settings.hooksVersion = HOOKS_VERSION;
         settings.hooks = {
             SubagentStart: [
                 {
@@ -1259,7 +1312,13 @@ async function main() {
         }
         fs.writeFileSync(settingsPath, JSON.stringify(settings, null, 2));
         console.log('✅ Configured search enforcement hook');
-        // === INSTALL: Copy skills directory ===
+        installSkills(claudeDir, packageSkillsDir);
+        console.log('\n✅ Setup complete!\n');
+        console.log('ℹ️  Uses Skills (guidance) + hooks (auto-capture with LLM classification).');
+        console.log('Restart Claude Code to activate.\n');
+    }
+    // === INSTALL: Copy skills directory (idempotent overwrite) ===
+    function installSkills(claudeDir, packageSkillsDir) {
         if (fs.existsSync(packageSkillsDir)) {
             const skillsDir = path.join(claudeDir, 'skills');
             copyDirRecursive(packageSkillsDir, skillsDir);
@@ -1268,9 +1327,6 @@ async function main() {
         else {
             console.log(`⚠️  Skills not found at: ${packageSkillsDir}`);
         }
-        console.log('\n✅ Setup complete!\n');
-        console.log('ℹ️  Uses Skills (guidance) + hooks (auto-capture with LLM classification).');
-        console.log('Restart Claude Code to activate.\n');
     }
     // Setup command - shows activation instructions or installs skills
     program
@@ -1283,24 +1339,32 @@ async function main() {
             installSkillsAndHook();
         }
         else {
-            // Show activation instructions
+            // Show activation instructions. Registration uses the global
+            // `claude-recall` binary, NOT `npx ... @latest`: npx resolves through
+            // any stale project-local install (shadow trap) and @latest hits the
+            // registry on every server spawn. Consecutive commands are printed
+            // flush-left as one contiguous block so they can be copy-pasted in
+            // one go.
             console.log('\n✅ Claude Recall Setup\n');
             console.log('━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━');
-            console.log('📌 ACTIVATE CLAUDE RECALL:');
+            console.log('📌 ACTIVATE CLAUDE RECALL (run in each project):');
             console.log('━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━');
             console.log('');
-            console.log('  claude mcp add claude-recall -- npx -y claude-recall@latest mcp start');
+            console.log('claude-recall setup --install');
+            console.log('claude mcp add claude-recall -- claude-recall mcp start');
             console.log('');
             console.log('  Then restart Claude Code (exit and re-enter the session).');
             console.log('');
             console.log('━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━');
             console.log('');
-            console.log('🔄 Already registered? Remove and re-add:');
-            console.log('  claude mcp remove claude-recall');
-            console.log('  claude mcp add claude-recall -- npx -y claude-recall@latest mcp start');
+            console.log('🔄 Registered under an old npx-based command? Remove and re-add:');
+            console.log('');
+            console.log('claude mcp remove claude-recall');
+            console.log('claude mcp add claude-recall -- claude-recall mcp start');
+            console.log('');
+            console.log('🛑 Stop a running old instance:');
             console.log('');
-            console.log('🛑 Stop old instance:');
-            console.log('  npx claude-recall mcp stop');
+            console.log('claude-recall mcp stop');
             console.log('');
         }
         process.exit(0);
@@ -1372,7 +1436,7 @@ async function main() {
         }
         if (!settingsPath) {
             console.log('❌ No .claude/settings.json found in directory tree');
-            console.log('   Run: npx claude-recall repair\n');
+            console.log('   Run: claude-recall repair\n');
             return;
         }
         console.log(`✅ Found settings: ${settingsPath}`);
@@ -1429,7 +1493,7 @@ async function main() {
             }
         }
         if (hasIssues) {
-            console.log('\n⚠️  Issues found. Run: npx claude-recall repair\n');
+            console.log('\n⚠️  Issues found. Run: claude-recall repair\n');
         }
         else {
             console.log('\n✅ All hooks OK!\n');
@@ -1460,7 +1524,7 @@ async function main() {
         }
         if (!enforcerPath) {
             console.log('❌ Could not find search_enforcer.py');
-            console.log('   Run: npx claude-recall repair\n');
+            console.log('   Run: claude-recall repair\n');
             return;
         }
         console.log(`📍 Enforcer: ${enforcerPath}`);
@@ -1544,7 +1608,7 @@ async function main() {
         }
         else {
             console.log('❌ Some tests failed. Check hook configuration.\n');
-            console.log('Run: npx claude-recall repair\n');
+            console.log('Run: claude-recall repair\n');
         }
     }
     // Hooks command group
@@ -1644,7 +1708,7 @@ async function main() {
         console.log('\n📋 Auto-Generated Skills\n');
         if (skills.length === 0) {
             console.log('No auto-generated skills found.\n');
-            console.log('Run `npx claude-recall skills generate` to create skills from memories.\n');
+            console.log('Run `claude-recall skills generate` to create skills from memories.\n');
         }
         else {
             for (const skill of skills) {
@@ -1761,7 +1825,7 @@ async function main() {
         .action((query, options) => {
         const cli = new ClaudeRecallCLI(program.opts());
         cli.search(query, {
-            limit: parseInt(options.limit),
+            limit: (0, parse_utils_1.parsePositiveInt)(options.limit, 'limit', 10),
             json: options.json,
             project: options.project,
             global: options.global
@@ -1791,7 +1855,7 @@ async function main() {
         .action((options) => {
         const cli = new ClaudeRecallCLI(program.opts());
         cli.showFailures({
-            limit: parseInt(options.limit),
+            limit: (0, parse_utils_1.parsePositiveInt)(options.limit, 'limit', 10),
             project: options.project
         });
         process.exit(0);
@@ -1805,7 +1869,7 @@ async function main() {
         .action((options) => {
         const cli = new ClaudeRecallCLI(program.opts());
         cli.showOutcomes({
-            limit: parseInt(options.limit),
+            limit: (0, parse_utils_1.parsePositiveInt)(options.limit, 'limit', 10),
             section: options.section
         });
         process.exit(0);
@@ -1824,8 +1888,8 @@ async function main() {
         const cli = new ClaudeRecallCLI(program.opts());
         cli.demoteRules({
             dryRun: options.dryRun,
-            minLoads: parseInt(options.minLoads),
-            minAgeDays: parseInt(options.minAgeDays),
+            minLoads: (0, parse_utils_1.parsePositiveInt)(options.minLoads, 'min-loads', 20),
+            minAgeDays: (0, parse_utils_1.parsePositiveInt)(options.minAgeDays, 'min-age-days', 7),
         });
         process.exit(0);
     });
@@ -1846,7 +1910,7 @@ async function main() {
         const cli = new ClaudeRecallCLI(program.opts());
         cli.dedupSimilarRules({
             dryRun: options.dryRun,
-            threshold: parseFloat(options.threshold),
+            threshold: (0, parse_utils_1.parseUnitFloat)(options.threshold, 'threshold', 0.65),
         });
         process.exit(0);
     });
@@ -1887,10 +1951,11 @@ async function main() {
     // Import command
     program
         .command('import <input>')
-        .description('Import memories from file')
-        .action(async (input) => {
+        .description('Import memories from file (original project scoping preserved)')
+        .option('--project <id>', 'Rescope all imported memories to this project ID')
+        .action(async (input, options) => {
         const cli = new ClaudeRecallCLI(program.opts());
-        await cli.import(input);
+        await cli.import(input, options);
         process.exit(0);
     });
     // Clear command
@@ -1993,7 +2058,7 @@ async function main() {
         const cli = new ClaudeRecallCLI(program.opts());
         await cli.store(content, {
             type: options.type,
-            confidence: parseFloat(options.confidence),
+            confidence: (0, parse_utils_1.parseUnitFloat)(options.confidence, 'confidence', 0.8),
             metadata: options.metadata
         });
         process.exit(0);

package/dist/cli/commands/mcp-commands.js

@@ -102,7 +102,7 @@ class MCPCommands {
         else {
             console.log();
             console.log(chalk_1.default.yellow('⚠ Project not registered in registry'));
-            console.log(chalk_1.default.gray('  Run `npx claude-recall project register` to register'));
+            console.log(chalk_1.default.gray('  Run `claude-recall project register` to register'));
         }
         console.log();
     }
@@ -135,7 +135,7 @@ class MCPCommands {
                 console.log(`  ${chalk_1.default.gray(server.projectId.padEnd(40))} PID: ${chalk_1.default.gray(server.pid)} (not running)`);
             }
             console.log();
-            console.log(chalk_1.default.yellow(`💡 Run 'npx claude-recall mcp cleanup' to remove stale PID files`));
+            console.log(chalk_1.default.yellow(`💡 Run 'claude-recall mcp cleanup' to remove stale PID files`));
             console.log();
         }
         // Show registered projects that don't have running servers
@@ -147,7 +147,7 @@ class MCPCommands {
                 console.log(`  ${chalk_1.default.gray(projectId.padEnd(40))} v${entry.version}`);
             }
             console.log();
-            console.log(chalk_1.default.gray(`💡 Run 'npx claude-recall project list' for detailed registry info`));
+            console.log(chalk_1.default.gray(`💡 Run 'claude-recall project list' for detailed registry info`));
             console.log();
         }
     }
@@ -173,19 +173,25 @@ class MCPCommands {
             return;
         }
         const signal = options.force ? 'SIGKILL' : 'SIGTERM';
-        console.log(`Sending ${signal} to PID ${chalk_1.default.yellow(status.pid)}...`);
+        const pid = status.pid;
+        console.log(`Sending ${signal} to PID ${chalk_1.default.yellow(pid)}...`);
         try {
-            this.processManager.killProcess(status.pid, options.force || false);
-            this.processManager.removePidFile(projectId);
-            // Give it a moment to shut down
-            await new Promise(resolve => setTimeout(resolve, 1000));
-            // Verify it stopped
-            const newStatus = this.processManager.getServerStatus(projectId);
-            if (!newStatus.isRunning) {
+            this.processManager.killProcess(pid, options.force || false);
+            // Verify death against the SAVED pid, polling up to 5s. The previous
+            // code removed the PID file first and then "verified" by re-reading it,
+            // so isRunning was always false and "stopped successfully" printed even
+            // if the process ignored SIGTERM.
+            const deadline = Date.now() + 5000;
+            while (this.processManager.isProcessRunning(pid) && Date.now() < deadline) {
+                await new Promise(resolve => setTimeout(resolve, 100));
+            }
+            if (!this.processManager.isProcessRunning(pid)) {
+                this.processManager.removePidFile(projectId);
                 console.log(chalk_1.default.green('✓ Server stopped successfully'));
             }
             else {
-                console.log(chalk_1.default.yellow('⚠ Server may still be running. Try --force flag.'));
+                // Keep the PID file — the server is still alive and tracked
+                console.log(chalk_1.default.yellow(`⚠ PID ${pid} is still running after ${signal}. Try --force flag.`));
             }
         }
         catch (error) {
@@ -208,7 +214,7 @@ class MCPCommands {
             await new Promise(resolve => setTimeout(resolve, 2000));
         }
         console.log('\nTo start the server, run:');
-        console.log(chalk_1.default.cyan('  npx claude-recall mcp start'));
+        console.log(chalk_1.default.cyan('  claude-recall mcp start'));
         console.log();
         console.log(chalk_1.default.gray('Note: The MCP server is normally started automatically by Claude Code.'));
         console.log(chalk_1.default.gray('      You only need to run this manually for debugging purposes.'));