@tekmidian/pai 0.5.6 → 0.6.0

package/dist/cli/index.mjs

@@ -1,16 +1,19 @@
 #!/usr/bin/env node
-import { n as openRegistry } from "../db-4lSqLFb8.mjs";
+import { n as openRegistry } from "../db-BtuN768f.mjs";
 import { _ as warn, a as fmtDate, c as ok, d as scaffoldProjectDirs, f as shortenPath, i as err, l as renderTable, m as slugify, n as dim, o as header, p as slugFromPath, r as encodeDir, s as now, t as bold, u as resolvePath } from "../utils-QSfKagcj.mjs";
 import { a as slugify$1, i as parseSessionFilename, n as decodeEncodedDir, t as buildEncodedDirMap } from "../migrate-jokLenje.mjs";
 import { n as ensurePaiMarker, t as discoverPaiMarkers } from "../pai-marker-CXQPX2P6.mjs";
-import { n as openFederation } from "../db-Dp8VXIMR.mjs";
-import { a as indexProject, n as embedChunks, r as indexAll } from "../indexer-CMPOiY1r.mjs";
+import { n as openFederation } from "../db-DdUperSl.mjs";
+import "../helpers-BEST-4Gx.mjs";
+import { i as indexProject, n as indexAll, t as embedChunks } from "../sync-BOsnEj2-.mjs";
 import "../embeddings-DGRAPAYb.mjs";
-import { n as populateSlugs, r as searchMemory } from "../search-_oHfguA5.mjs";
-import { a as expandHome, i as ensureConfigDir, n as CONFIG_FILE$2, o as loadConfig$1, t as CONFIG_DIR } from "../config-Cf92lGX_.mjs";
-import { n as formatDetection, r as formatDetectionJson, t as detectProject } from "../detect-BU3Nx_2L.mjs";
-import { t as PaiClient } from "../ipc-client-Bjg_a1dc.mjs";
-import { t as createStorageBackend } from "../factory-Bzcy70G9.mjs";
+import { t as STOP_WORDS } from "../stop-words-BaMEGVeY.mjs";
+import { n as populateSlugs, r as searchMemory } from "../search-DC1qhkKn.mjs";
+import { n as formatDetection, r as formatDetectionJson, t as detectProject } from "../detect-CdaA48EI.mjs";
+import "../indexer-D53l5d1U.mjs";
+import { t as PaiClient } from "../ipc-client-CoyUHPod.mjs";
+import { a as expandHome, i as ensureConfigDir, n as CONFIG_FILE$2, o as loadConfig, t as CONFIG_DIR } from "../config-BuhHWyOK.mjs";
+import { t as createStorageBackend } from "../factory-Ygqe_bVZ.mjs";
 import { appendFileSync, chmodSync, copyFileSync, existsSync, lstatSync, mkdirSync, readFileSync, readdirSync, readlinkSync, renameSync, statSync, symlinkSync, unlinkSync, writeFileSync } from "node:fs";
 import { homedir, tmpdir } from "node:os";
 import { basename, dirname, join, relative, resolve } from "node:path";
@@ -19,6 +22,7 @@ import { Command } from "commander";
 import { fileURLToPath } from "node:url";
 import { execSync, spawnSync } from "node:child_process";
 import { createInterface } from "node:readline";
+import { createConnection } from "net";
 
 //#region src/session/promote.ts
 /**
@@ -119,7 +123,7 @@ function cmdPromote(db, opts) {
 }
 
 //#endregion
-//#region src/cli/commands/project.ts
+//#region src/cli/commands/project/helpers.ts
 function getProject$2(db, slug) {
 	const direct = db.prepare("SELECT * FROM projects WHERE slug = ?").get(slug);
 	if (direct) return direct;
@@ -167,6 +171,49 @@ function upsertTag$1(db, tagName) {
 	db.prepare("INSERT OR IGNORE INTO tags (name) VALUES (?)").run(tagName);
 	return db.prepare("SELECT id FROM tags WHERE name = ?").get(tagName).id;
 }
+
+//#endregion
+//#region src/cli/commands/project/commands.ts
+function levenshtein(a, b) {
+	const m = a.length;
+	const n = b.length;
+	const dp = Array.from({ length: m + 1 }, (_, i) => Array.from({ length: n + 1 }, (_, j) => i === 0 ? j : j === 0 ? i : 0));
+	for (let i = 1; i <= m; i++) for (let j = 1; j <= n; j++) dp[i][j] = a[i - 1] === b[j - 1] ? dp[i - 1][j - 1] : 1 + Math.min(dp[i - 1][j], dp[i][j - 1], dp[i - 1][j - 1]);
+	return dp[m][n];
+}
+function containsIgnoreCase(haystack, needle) {
+	return haystack.toLowerCase().includes(needle.toLowerCase());
+}
+function findProjectNotesDirs(project) {
+	const claudeProjects = join(homedir(), ".claude", "projects");
+	if (!existsSync(claudeProjects)) return [];
+	const results = [];
+	const rootEncoded = encodeDir(project.root_path);
+	try {
+		for (const entry of readdirSync(claudeProjects)) {
+			const full = join(claudeProjects, entry);
+			try {
+				if (!statSync(full).isDirectory()) continue;
+			} catch {
+				continue;
+			}
+			if (entry !== rootEncoded && !entry.startsWith(rootEncoded)) continue;
+			const notesPath = join(full, "Notes");
+			if (!existsSync(notesPath)) continue;
+			let noteCount = 0;
+			try {
+				noteCount = readdirSync(notesPath).filter((f) => f.endsWith(".md") || f.endsWith(".txt")).length;
+			} catch {}
+			results.push({
+				encodedDir: entry,
+				fullPath: full,
+				notesPath,
+				noteCount
+			});
+		}
+	} catch {}
+	return results;
+}
 function cmdAdd(db, rawPath, opts) {
 	const rootPath = resolvePath(rawPath);
 	const slug = opts.slug ?? slugFromPath(rootPath);
@@ -187,6 +234,15 @@ function cmdAdd(db, rawPath, opts) {
 		console.error(err(`Project already registered (slug: ${slug} or path: ${rootPath})`));
 		process.exit(1);
 	}
+	const dirName = basename(rootPath).toLowerCase();
+	const matches = db.prepare(`SELECT slug, root_path FROM projects WHERE status = 'active' AND slug != ?`).all(slug).filter((s) => basename(s.root_path).toLowerCase() === dirName || s.slug.replace(/-\d+$/, "") === slug.replace(/-\d+$/, ""));
+	if (matches.length > 0) {
+		console.log(warn(`Similar project(s) already registered:`));
+		for (const m of matches) console.log(dim(`  ${bold(m.slug)}  ${shortenPath(m.root_path, 50)}`));
+		console.log(dim(`  Consider: pai project alias ${matches[0].slug} <name> (to link them)`));
+		console.log(dim(`  Or: pai project archive ${slug} (if this is a duplicate)`));
+		console.log();
+	}
 	const ts = now();
 	db.prepare(`INSERT INTO projects
        (slug, display_name, root_path, encoded_dir, type, status, created_at, updated_at)
@@ -200,7 +256,7 @@ function cmdAdd(db, rawPath, opts) {
 	console.log(dim(`  Encoded dir:  ${encodedDir}`));
 	console.log(dim(`  Type:         ${type}`));
 }
-function cmdList$1(db, opts) {
+function cmdList$2(db, opts) {
 	let query = `
     SELECT p.*,
       (SELECT COUNT(*) FROM sessions s WHERE s.project_id = p.id) AS session_count,
@@ -378,142 +434,6 @@ function cmdEdit(db, slug, opts) {
 		console.log(ok(`Type updated: ${bold(opts.type)}`));
 	}
 }
-/**
-* Find Claude project dirs (~/.claude/projects/) that look like they belong
-* to a project based on encoded_dir prefix matching.
-*/
-function findOrphanedNotesDirs(project) {
-	const claudeProjects = join(homedir(), ".claude", "projects");
-	if (!existsSync(claudeProjects)) return [];
-	const expected = encodeDir(project.root_path);
-	const results = [];
-	try {
-		for (const entry of readdirSync(claudeProjects)) {
-			const full = join(claudeProjects, entry);
-			try {
-				if (!statSync(full).isDirectory()) continue;
-			} catch {
-				continue;
-			}
-			if (entry === expected || entry === project.encoded_dir) {
-				const notesDir = join(full, "Notes");
-				if (existsSync(notesDir)) results.push(notesDir);
-			}
-		}
-	} catch {}
-	return results;
-}
-/**
-* Try to find a moved project by looking for a directory with the same name
-* as the last path component in common nearby locations.
-*/
-function suggestMovedPath(project) {
-	const name = basename(project.root_path);
-	const candidates = [
-		join(homedir(), "dev", name),
-		join(homedir(), "dev", "ai", name),
-		join(homedir(), "Desktop", name),
-		join(homedir(), "Projects", name)
-	];
-	for (const c of candidates) if (existsSync(c)) return c;
-}
-function cmdHealth$1(db, opts) {
-	const rows = db.prepare(`SELECT p.*,
-         (SELECT COUNT(*) FROM sessions s WHERE s.project_id = p.id) AS session_count
-       FROM projects p
-       ORDER BY p.status ASC, p.updated_at DESC`).all();
-	const results = rows.map((project) => {
-		const pathExists = existsSync(project.root_path);
-		const orphaned = findOrphanedNotesDirs(project);
-		let category;
-		let suggestedPath;
-		if (pathExists) category = "active";
-		else {
-			suggestedPath = suggestMovedPath(project);
-			category = suggestedPath ? "stale" : "dead";
-		}
-		const claudeNotesExists = orphaned.length > 0;
-		return {
-			project,
-			category,
-			suggestedPath,
-			claudeNotesExists,
-			orphanedNotesDirs: orphaned
-		};
-	});
-	const filtered = opts.status ? results.filter((r) => r.category === opts.status) : results;
-	if (opts.json) {
-		console.log(JSON.stringify(filtered.map((r) => ({
-			slug: r.project.slug,
-			root_path: r.project.root_path,
-			status: r.project.status,
-			health: r.category,
-			session_count: r.project.session_count,
-			suggested_path: r.suggestedPath ?? null,
-			claude_notes_exists: r.claudeNotesExists,
-			orphaned_notes_dirs: r.orphanedNotesDirs
-		})), null, 2));
-		return;
-	}
-	const active = filtered.filter((r) => r.category === "active");
-	const stale = filtered.filter((r) => r.category === "stale");
-	const dead = filtered.filter((r) => r.category === "dead");
-	console.log();
-	console.log(header("  PAI Project Health Report"));
-	console.log();
-	console.log(`  ${chalk.green("Active:")} ${active.length}   ${chalk.yellow("Stale (moved?):")} ${stale.length}   ${chalk.red("Dead (missing):")} ${dead.length}`);
-	console.log();
-	if (active.length) {
-		console.log(bold("  Active projects (path exists):"));
-		const tableRows = active.map((r) => [
-			bold(r.project.slug),
-			dim(shortenPath(r.project.root_path, 50)),
-			String(r.project.session_count),
-			r.claudeNotesExists ? chalk.green("yes") : dim("no")
-		]);
-		console.log(renderTable([
-			"Slug",
-			"Path",
-			"Sessions",
-			"Claude Notes"
-		], tableRows).split("\n").map((l) => "  " + l).join("\n"));
-		console.log();
-	}
-	if (stale.length) {
-		console.log(warn("  Stale projects (path missing, possible new location found):"));
-		for (const r of stale) {
-			console.log(`    ${bold(r.project.slug)}`);
-			console.log(dim(`      Old path:   ${r.project.root_path}`));
-			console.log(chalk.cyan(`      Found at:   ${r.suggestedPath}`));
-			if (r.claudeNotesExists) console.log(chalk.green(`      Notes:      ${r.orphanedNotesDirs.join(", ")}`));
-			if (opts.fix && r.suggestedPath) {
-				const ts = now();
-				const newEncoded = encodeDir(r.suggestedPath);
-				db.prepare("UPDATE projects SET root_path = ?, encoded_dir = ?, updated_at = ? WHERE id = ?").run(r.suggestedPath, newEncoded, ts, r.project.id);
-				console.log(ok(`      Auto-fixed: updated path to ${r.suggestedPath}`));
-			} else if (r.suggestedPath) console.log(dim(`      Fix:        pai project move ${r.project.slug} ${r.suggestedPath}`));
-		}
-		console.log();
-	}
-	if (dead.length) {
-		console.log(err("  Dead projects (path missing, no match found):"));
-		for (const r of dead) {
-			console.log(`    ${bold(r.project.slug)}   ${dim(r.project.root_path)}`);
-			if (r.claudeNotesExists) console.log(chalk.yellow(`      Notes:  ${r.orphanedNotesDirs.join(", ")}`));
-			if (r.project.session_count === 0 && opts.fix) {
-				db.prepare("UPDATE projects SET status = 'archived', archived_at = ?, updated_at = ? WHERE id = ?").run(now(), now(), r.project.id);
-				console.log(ok("      Auto-fixed: archived (0 sessions, path gone)"));
-			} else console.log(dim(`      Fix:    pai project archive ${r.project.slug}  (or  pai project move ...)`));
-		}
-		console.log();
-	}
-	const summary = `  ${rows.length} total: ${active.length} active, ${stale.length} stale, ${dead.length} dead`;
-	console.log(dim(summary));
-	if (!opts.fix && (stale.length > 0 || dead.length > 0)) {
-		console.log();
-		console.log(warn("  Run with --fix to auto-remediate where possible."));
-	}
-}
 function cmdDetect(db, pathArg, opts) {
 	const cwd = pathArg ? resolvePath(pathArg) : process.cwd();
 	const detection = detectProject(db, cwd);
@@ -539,40 +459,6 @@ function cmdDetect(db, pathArg, opts) {
 	console.log(formatDetection(detection).split("\n").map((l) => "  " + l).join("\n"));
 	console.log();
 }
-/**
-* Find all ~/.claude/projects/ encoded dirs whose name encodes to a path
-* that is a child-of or exact-match of the given project's root_path.
-*/
-function findProjectNotesDirs(project) {
-	const claudeProjects = join(homedir(), ".claude", "projects");
-	if (!existsSync(claudeProjects)) return [];
-	const results = [];
-	const rootEncoded = encodeDir(project.root_path);
-	try {
-		for (const entry of readdirSync(claudeProjects)) {
-			const full = join(claudeProjects, entry);
-			try {
-				if (!statSync(full).isDirectory()) continue;
-			} catch {
-				continue;
-			}
-			if (entry !== rootEncoded && !entry.startsWith(rootEncoded)) continue;
-			const notesPath = join(full, "Notes");
-			if (!existsSync(notesPath)) continue;
-			let noteCount = 0;
-			try {
-				noteCount = readdirSync(notesPath).filter((f) => f.endsWith(".md") || f.endsWith(".txt")).length;
-			} catch {}
-			results.push({
-				encodedDir: entry,
-				fullPath: full,
-				notesPath,
-				noteCount
-			});
-		}
-	} catch {}
-	return results;
-}
 function cmdConsolidate(db, identifier, opts) {
 	const project = resolveIdentifier(db, identifier) ?? requireProject(db, identifier);
 	console.log();
@@ -628,22 +514,6 @@ function cmdConsolidate(db, identifier, opts) {
 	console.log();
 	console.log(ok(`  Consolidated ${movedCount} file(s) into ${canonicalNotes}`));
 }
-/**
-* Simple Levenshtein distance for "did you mean?" suggestions.
-*/
-function levenshtein(a, b) {
-	const m = a.length;
-	const n = b.length;
-	const dp = Array.from({ length: m + 1 }, (_, i) => Array.from({ length: n + 1 }, (_, j) => i === 0 ? j : j === 0 ? i : 0));
-	for (let i = 1; i <= m; i++) for (let j = 1; j <= n; j++) dp[i][j] = a[i - 1] === b[j - 1] ? dp[i - 1][j - 1] : 1 + Math.min(dp[i - 1][j], dp[i][j - 1], dp[i - 1][j - 1]);
-	return dp[m][n];
-}
-/**
-* Check if `needle` appears as a substring (case-insensitive) in `haystack`.
-*/
-function containsIgnoreCase(haystack, needle) {
-	return haystack.toLowerCase().includes(needle.toLowerCase());
-}
 function cmdGo(db, query) {
 	const all = db.prepare("SELECT * FROM projects WHERE status = 'active' ORDER BY updated_at DESC").all();
 	if (!all.length) {
@@ -689,46 +559,581 @@ function cmdGo(db, query) {
 	}
 	process.exit(1);
 }
-function registerProjectCommands(projectCmd, getDb) {
-	projectCmd.command("add <path>").description("Register a project directory in the PAI registry").option("--slug <slug>", "Override auto-generated slug").option("--type <type>", "Project type: local | central | obsidian-linked | external", "local").option("--display-name <name>", "Human-readable display name").action((rawPath, opts) => {
-		cmdAdd(getDb(), rawPath, opts);
-	});
-	projectCmd.command("list").description("List registered projects").option("--status <status>", "Filter by status: active | archived").option("--tag <tag>", "Filter by tag").option("--type <type>", "Filter by type").action((opts) => {
-		cmdList$1(getDb(), opts);
-	});
-	projectCmd.command("info <slug>").description("Show full details for a project").action((slug) => {
-		cmdInfo$1(getDb(), slug);
-	});
-	projectCmd.command("archive <slug>").description("Archive a project").action((slug) => {
-		cmdArchive(getDb(), slug);
-	});
-	projectCmd.command("unarchive <slug>").description("Restore an archived project to active status").action((slug) => {
-		cmdUnarchive(getDb(), slug);
-	});
-	projectCmd.command("move <slug> <new-path>").description("Update the root path for a project").action((slug, newPath) => {
-		cmdMove(getDb(), slug, newPath);
-	});
-	projectCmd.command("tag <slug> <tags...>").description("Add one or more tags to a project").action((slug, tags) => {
-		cmdTag$1(getDb(), slug, tags);
-	});
-	projectCmd.command("alias <slug> <alias>").description("Register an alternative slug for a project").action((slug, alias) => {
-		cmdAlias(getDb(), slug, alias);
-	});
-	projectCmd.command("edit <slug>").description("Edit project metadata").option("--display-name <name>", "New display name").option("--type <type>", "New type").action((slug, opts) => {
-		cmdEdit(getDb(), slug, opts);
-	});
-	projectCmd.command("cd <identifier>").description("Print the root path for a project (use with: cd $(pai project cd <id>))").action((identifier) => {
-		const project = resolveIdentifier(getDb(), identifier);
-		if (!project) {
-			console.error(`Project not found: ${identifier}`);
-			process.exit(1);
-		}
-		process.stdout.write(project.root_path + "\n");
-	});
-	projectCmd.command("detect [path]").description("Detect which registered project the given path (or CWD) belongs to").option("--json", "Output raw JSON instead of human-readable text").action((pathArg, opts) => {
-		cmdDetect(getDb(), pathArg, opts);
-	});
-	projectCmd.command("health").description("Audit all registered projects: check which paths still exist, find moved/dead projects").option("--fix", "Auto-remediate where possible (update moved paths, archive dead zero-session projects)").option("--json", "Output raw JSON report").option("--status <category>", "Filter output to: active | stale | dead").action((opts) => {
+
+//#endregion
+//#region src/cli/commands/project/session-config.ts
+const CONFIG_OPTIONS = [
+	{
+		key: "permission",
+		type: "string",
+		description: "Permission preset: full | trusted | default",
+		examples: [
+			"full",
+			"trusted",
+			"default"
+		]
+	},
+	{
+		key: "flags",
+		type: "string",
+		description: "Raw Claude CLI flags",
+		examples: ["--dangerously-skip-permissions", "--allowedTools Edit,Read"]
+	},
+	{
+		key: "env",
+		type: "object",
+		description: "Environment variables as key=value pairs",
+		examples: ["IS_SANDBOX=1", "CLAUDE_MODEL=opus"]
+	},
+	{
+		key: "autoStart",
+		type: "boolean",
+		description: "Auto-start session (skip interactive prompt)",
+		examples: ["true", "false"]
+	},
+	{
+		key: "prompt",
+		type: "string",
+		description: "Initial prompt sent to Claude on launch",
+		examples: [
+			"go",
+			"continue",
+			"run tests"
+		]
+	},
+	{
+		key: "model",
+		type: "string",
+		description: "Model override for the session",
+		examples: [
+			"opus",
+			"sonnet",
+			"haiku"
+		]
+	}
+];
+const PERMISSION_PRESETS = {
+	full: {
+		permission: "full",
+		flags: "--dangerously-skip-permissions",
+		env: { IS_SANDBOX: "1" },
+		autoStart: true,
+		prompt: "go"
+	},
+	trusted: {
+		permission: "trusted",
+		flags: "",
+		env: {},
+		autoStart: true,
+		prompt: "go"
+	},
+	default: {
+		permission: "default",
+		flags: "",
+		env: {},
+		autoStart: false
+	}
+};
+function getSessionConfig(project) {
+	return project.session_config ? JSON.parse(project.session_config) : {};
+}
+function getGlobalDefaults() {
+	try {
+		const configPath = join(homedir(), ".config", "pai", "config.json");
+		if (existsSync(configPath)) return JSON.parse(readFileSync(configPath, "utf-8")).sessionDefaults ?? {};
+	} catch {}
+	return {};
+}
+function saveGlobalDefaults(defaults) {
+	const configPath = join(homedir(), ".config", "pai", "config.json");
+	let config = {};
+	try {
+		if (existsSync(configPath)) config = JSON.parse(readFileSync(configPath, "utf-8"));
+	} catch {}
+	config.sessionDefaults = defaults;
+	mkdirSync(join(homedir(), ".config", "pai"), { recursive: true });
+	writeFileSync(configPath, JSON.stringify(config, null, 2) + "\n");
+}
+function applyPreset(config, preset) {
+	const presetConfig = PERMISSION_PRESETS[preset];
+	if (!presetConfig) return {
+		...config,
+		permission: "custom",
+		flags: preset
+	};
+	return {
+		...config,
+		...presetConfig
+	};
+}
+function parseConfigValue(key, value) {
+	const option = CONFIG_OPTIONS.find((o) => o.key === key);
+	if (!option) return value;
+	switch (option.type) {
+		case "boolean": return value === "true" || value === "1" || value === "yes";
+		case "object":
+			if (key === "env") {
+				const [k, ...vParts] = value.split("=");
+				return { [k]: vParts.join("=") || "1" };
+			}
+			return value;
+		default: return value;
+	}
+}
+function cmdName(db, identifier, shortname, opts) {
+	const project = resolveIdentifier(db, identifier) ?? requireProject(db, identifier);
+	if (!/^[a-zA-Z][a-zA-Z0-9_-]*$/.test(shortname)) {
+		console.error(err(`Invalid name "${shortname}". Use letters, digits, hyphens, underscores. Must start with a letter.`));
+		process.exit(1);
+	}
+	if (db.prepare("SELECT id FROM projects WHERE slug = ? AND id != ?").get(shortname, project.id)) {
+		console.error(err(`"${shortname}" is already a project slug.`));
+		process.exit(1);
+	}
+	const conflictAlias = db.prepare("SELECT project_id FROM aliases WHERE alias = ?").get(shortname);
+	if (conflictAlias && conflictAlias.project_id !== project.id) {
+		console.error(err(`"${shortname}" is already used by another project.`));
+		process.exit(1);
+	}
+	if (!conflictAlias) db.prepare("INSERT INTO aliases (alias, project_id) VALUES (?, ?)").run(shortname, project.id);
+	if (opts.permission) {
+		const config = applyPreset(getSessionConfig(project), opts.permission);
+		db.prepare("UPDATE projects SET session_config = ?, updated_at = ? WHERE id = ?").run(JSON.stringify(config), now(), project.id);
+	}
+	console.log(ok(`Named: ${bold(shortname)} → ${project.slug} (${shortenPath(project.root_path, 50)})`));
+	if (opts.permission) console.log(dim(`  Permission: ${opts.permission}`));
+}
+function cmdUnname(db, shortname) {
+	const alias = db.prepare("SELECT project_id FROM aliases WHERE alias = ?").get(shortname);
+	if (!alias) {
+		console.error(err(`No named project found: "${shortname}"`));
+		process.exit(1);
+	}
+	db.prepare("DELETE FROM aliases WHERE alias = ?").run(shortname);
+	const remaining = db.prepare("SELECT COUNT(*) AS cnt FROM aliases WHERE project_id = ?").get(alias.project_id);
+	console.log(ok(`Removed name: ${bold(shortname)}`));
+	if (remaining.cnt === 0) console.log(dim("  Project has no remaining names."));
+}
+function cmdNames(db, opts) {
+	const rows = db.prepare(`
+    SELECT p.*, a.alias AS name,
+      (SELECT COUNT(*) FROM sessions s WHERE s.project_id = p.id) AS session_count,
+      (SELECT MAX(s.created_at) FROM sessions s WHERE s.project_id = p.id) AS last_active
+    FROM projects p
+    JOIN aliases a ON a.project_id = p.id
+    WHERE p.status = 'active'
+    ORDER BY p.updated_at DESC
+  `).all();
+	if (opts.json) {
+		const grouped = /* @__PURE__ */ new Map();
+		for (const row of rows) if (!grouped.has(row.id)) grouped.set(row.id, {
+			name: row.name,
+			names: [row.name],
+			slug: row.slug,
+			display_name: row.display_name,
+			root_path: row.root_path,
+			session_count: row.session_count,
+			last_active: row.last_active ? new Date(row.last_active).toISOString() : null,
+			session_config: row.session_config ? JSON.parse(row.session_config) : null
+		});
+		else grouped.get(row.id).names.push(row.name);
+		console.log(JSON.stringify([...grouped.values()], null, 2));
+		return;
+	}
+	if (!rows.length) {
+		console.log(warn("No named projects. Use: pai project name <slug-or-number> <shortname>"));
+		return;
+	}
+	const seen = /* @__PURE__ */ new Set();
+	const tableRows = [];
+	for (const row of rows) {
+		if (seen.has(row.id)) continue;
+		seen.add(row.id);
+		const allNames = rows.filter((r) => r.id === row.id).map((r) => r.name);
+		const perm = (row.session_config ? JSON.parse(row.session_config) : null)?.permission ?? dim("default");
+		tableRows.push([
+			bold(allNames.join(", ")),
+			row.slug,
+			dim(shortenPath(row.root_path, 40)),
+			typeof perm === "string" ? perm : dim("default"),
+			String(row.session_count),
+			fmtDate(row.last_active)
+		]);
+	}
+	console.log();
+	console.log(header("  Named Projects"));
+	console.log();
+	console.log(renderTable([
+		"Name(s)",
+		"Slug",
+		"Path",
+		"Permission",
+		"Sessions",
+		"Last Active"
+	], tableRows));
+	console.log();
+	console.log(dim(`  ${tableRows.length} named project(s)`));
+}
+function cmdConfig(db, identifier, opts) {
+	if (opts.options) {
+		if (opts.json) {
+			console.log(JSON.stringify({
+				options: CONFIG_OPTIONS,
+				presets: Object.entries(PERMISSION_PRESETS).map(([name, config]) => ({
+					name,
+					...config
+				}))
+			}, null, 2));
+			return;
+		}
+		console.log();
+		console.log(header("  Session Config Options"));
+		console.log();
+		console.log(bold("  Available keys:"));
+		console.log();
+		for (const opt of CONFIG_OPTIONS) {
+			console.log(`    ${bold(opt.key.padEnd(14))} ${dim(`(${opt.type})`)}  ${opt.description}`);
+			console.log(`    ${" ".repeat(14)}        ${dim("e.g.")} ${opt.examples.map((e) => chalk.cyan(e)).join(", ")}`);
+		}
+		console.log();
+		console.log(bold("  Permission presets:"));
+		console.log();
+		for (const [name, config] of Object.entries(PERMISSION_PRESETS)) {
+			const parts = [];
+			if (config.flags) parts.push(`flags: ${config.flags}`);
+			if (config.env && Object.keys(config.env).length) parts.push(`env: ${Object.entries(config.env).map(([k, v]) => `${k}=${v}`).join(" ")}`);
+			if (config.autoStart) parts.push("autoStart");
+			if (config.prompt) parts.push(`prompt: "${config.prompt}"`);
+			console.log(`    ${bold(name.padEnd(10))} ${dim(parts.join(", ") || "(vanilla)")}`);
+		}
+		console.log();
+		return;
+	}
+	if (opts.defaults) {
+		let defaults = getGlobalDefaults();
+		if (opts.reset) {
+			saveGlobalDefaults({});
+			console.log(ok("Global session defaults reset."));
+			return;
+		}
+		if (opts.preset) {
+			defaults = applyPreset(defaults, opts.preset);
+			saveGlobalDefaults(defaults);
+			console.log(ok(`Global defaults set to preset: ${bold(opts.preset)}`));
+			return;
+		}
+		if (opts.set?.length) {
+			for (const pair of opts.set) {
+				const eqIdx = pair.indexOf("=");
+				if (eqIdx === -1) {
+					console.error(err(`Invalid format: "${pair}". Use key=value.`));
+					continue;
+				}
+				const key = pair.substring(0, eqIdx);
+				const value = pair.substring(eqIdx + 1);
+				if (!CONFIG_OPTIONS.find((o) => o.key === key)) {
+					console.error(err(`Unknown key: "${key}". Run: pai project config --options`));
+					continue;
+				}
+				if (key === "env") defaults.env = {
+					...defaults.env ?? {},
+					...parseConfigValue("env", value)
+				};
+				else defaults[key] = parseConfigValue(key, value);
+			}
+			saveGlobalDefaults(defaults);
+			console.log(ok("Global defaults updated."));
+		}
+		if (opts.unset?.length) {
+			for (const key of opts.unset) if (key.startsWith("env.")) {
+				const envKey = key.substring(4);
+				if (defaults.env) delete defaults.env[envKey];
+			} else delete defaults[key];
+			saveGlobalDefaults(defaults);
+			console.log(ok("Global defaults updated."));
+		}
+		if (opts.json) console.log(JSON.stringify(defaults, null, 2));
+		else {
+			console.log();
+			console.log(header("  Global Session Defaults"));
+			console.log();
+			if (Object.keys(defaults).length === 0) {
+				console.log(dim("  No defaults set. New sessions use vanilla Claude."));
+				console.log(dim("  Set with: pai project config --defaults --preset full"));
+			} else for (const [key, value] of Object.entries(defaults)) {
+				const display = typeof value === "object" ? JSON.stringify(value) : String(value);
+				console.log(`    ${bold(key.padEnd(14))} ${display}`);
+			}
+			console.log();
+		}
+		return;
+	}
+	if (!identifier) {
+		console.error(err("Specify a project: pai project config <name-or-slug>"));
+		console.error(dim("  Or use --defaults for global defaults, --options for available keys."));
+		process.exit(1);
+	}
+	const project = resolveIdentifier(db, identifier) ?? requireProject(db, identifier);
+	let config = getSessionConfig(project);
+	if (opts.reset) {
+		db.prepare("UPDATE projects SET session_config = NULL, updated_at = ? WHERE id = ?").run(now(), project.id);
+		console.log(ok(`Config reset for ${bold(project.slug)}. Will use global defaults.`));
+		return;
+	}
+	if (opts.preset) {
+		config = applyPreset(config, opts.preset);
+		db.prepare("UPDATE projects SET session_config = ?, updated_at = ? WHERE id = ?").run(JSON.stringify(config), now(), project.id);
+		console.log(ok(`Applied preset ${bold(opts.preset)} to ${bold(project.slug)}`));
+	}
+	if (opts.set?.length) {
+		for (const pair of opts.set) {
+			const eqIdx = pair.indexOf("=");
+			if (eqIdx === -1) {
+				console.error(err(`Invalid format: "${pair}". Use key=value.`));
+				continue;
+			}
+			const key = pair.substring(0, eqIdx);
+			const value = pair.substring(eqIdx + 1);
+			if (!CONFIG_OPTIONS.find((o) => o.key === key)) {
+				console.error(err(`Unknown key: "${key}". Run: pai project config --options`));
+				continue;
+			}
+			if (key === "env") config.env = {
+				...config.env ?? {},
+				...parseConfigValue("env", value)
+			};
+			else config[key] = parseConfigValue(key, value);
+		}
+		db.prepare("UPDATE projects SET session_config = ?, updated_at = ? WHERE id = ?").run(JSON.stringify(config), now(), project.id);
+		console.log(ok(`Config updated for ${bold(project.slug)}`));
+	}
+	if (opts.unset?.length) {
+		for (const key of opts.unset) if (key.startsWith("env.")) {
+			const envKey = key.substring(4);
+			if (config.env) delete config.env[envKey];
+		} else delete config[key];
+		db.prepare("UPDATE projects SET session_config = ?, updated_at = ? WHERE id = ?").run(JSON.stringify(config), now(), project.id);
+		console.log(ok(`Config updated for ${bold(project.slug)}`));
+	}
+	const effective = {
+		...getGlobalDefaults(),
+		...config
+	};
+	const aliases = getProjectAliases(db, project.id);
+	if (opts.json) {
+		console.log(JSON.stringify({
+			project: project.slug,
+			names: aliases,
+			root_path: project.root_path,
+			config,
+			global_defaults: getGlobalDefaults(),
+			effective
+		}, null, 2));
+		return;
+	}
+	console.log();
+	console.log(header(`  Config: ${project.slug}`));
+	if (aliases.length) console.log(dim(`  Names: ${aliases.join(", ")}`));
+	console.log(dim(`  Path: ${project.root_path}`));
+	console.log();
+	if (Object.keys(config).length === 0) console.log(dim("  No project-specific config. Using global defaults."));
+	else {
+		console.log(bold("  Project config:"));
+		for (const [key, value] of Object.entries(config)) {
+			const display = typeof value === "object" ? JSON.stringify(value) : String(value);
+			console.log(`    ${bold(key.padEnd(14))} ${display}`);
+		}
+	}
+	const globalDefaults = getGlobalDefaults();
+	if (Object.keys(globalDefaults).length > 0) {
+		console.log();
+		console.log(dim("  Global defaults (overridden by project config):"));
+		for (const [key, value] of Object.entries(globalDefaults)) {
+			const overridden = key in config;
+			const display = typeof value === "object" ? JSON.stringify(value) : String(value);
+			console.log(`    ${dim(key.padEnd(14))} ${overridden ? chalk.strikethrough(display) + " " + dim("(overridden)") : display}`);
+		}
+	}
+	console.log();
+	console.log(bold("  Effective (what AIBroker uses):"));
+	for (const [key, value] of Object.entries(effective)) {
+		const display = typeof value === "object" ? JSON.stringify(value) : String(value);
+		console.log(`    ${bold(key.padEnd(14))} ${display}`);
+	}
+	console.log();
+}
+
+//#endregion
+//#region src/cli/commands/project/health.ts
+function findOrphanedNotesDirs(project) {
+	const claudeProjects = join(homedir(), ".claude", "projects");
+	if (!existsSync(claudeProjects)) return [];
+	const expected = encodeDir(project.root_path);
+	const results = [];
+	try {
+		for (const entry of readdirSync(claudeProjects)) {
+			const full = join(claudeProjects, entry);
+			try {
+				if (!statSync(full).isDirectory()) continue;
+			} catch {
+				continue;
+			}
+			if (entry === expected || entry === project.encoded_dir) {
+				const notesDir = join(full, "Notes");
+				if (existsSync(notesDir)) results.push(notesDir);
+			}
+		}
+	} catch {}
+	return results;
+}
+function suggestMovedPath(project) {
+	const name = basename(project.root_path);
+	const candidates = [
+		join(homedir(), "dev", name),
+		join(homedir(), "dev", "ai", name),
+		join(homedir(), "Desktop", name),
+		join(homedir(), "Projects", name)
+	];
+	for (const candidate of candidates) if (existsSync(candidate)) return candidate;
+}
+function cmdHealth$1(db, opts) {
+	const rows = db.prepare(`SELECT p.*,
+         (SELECT COUNT(*) FROM sessions s WHERE s.project_id = p.id) AS session_count
+       FROM projects p
+       ORDER BY p.status ASC, p.updated_at DESC`).all();
+	const results = rows.map((project) => {
+		const pathExists = existsSync(project.root_path);
+		const orphaned = findOrphanedNotesDirs(project);
+		let category;
+		let suggestedPath;
+		if (pathExists) category = "active";
+		else {
+			suggestedPath = suggestMovedPath(project);
+			category = suggestedPath ? "stale" : "dead";
+		}
+		return {
+			project,
+			category,
+			suggestedPath,
+			claudeNotesExists: orphaned.length > 0,
+			orphanedNotesDirs: orphaned
+		};
+	});
+	const filtered = opts.status ? results.filter((r) => r.category === opts.status) : results;
+	if (opts.json) {
+		console.log(JSON.stringify(filtered.map((r) => ({
+			slug: r.project.slug,
+			root_path: r.project.root_path,
+			status: r.project.status,
+			health: r.category,
+			session_count: r.project.session_count,
+			suggested_path: r.suggestedPath ?? null,
+			claude_notes_exists: r.claudeNotesExists,
+			orphaned_notes_dirs: r.orphanedNotesDirs
+		})), null, 2));
+		return;
+	}
+	const active = filtered.filter((r) => r.category === "active");
+	const stale = filtered.filter((r) => r.category === "stale");
+	const dead = filtered.filter((r) => r.category === "dead");
+	console.log();
+	console.log(header("  PAI Project Health Report"));
+	console.log();
+	console.log(`  ${chalk.green("Active:")} ${active.length}   ${chalk.yellow("Stale (moved?):")} ${stale.length}   ${chalk.red("Dead (missing):")} ${dead.length}`);
+	console.log();
+	if (active.length) {
+		console.log(bold("  Active projects (path exists):"));
+		const tableRows = active.map((r) => [
+			bold(r.project.slug),
+			dim(shortenPath(r.project.root_path, 50)),
+			String(r.project.session_count),
+			r.claudeNotesExists ? chalk.green("yes") : dim("no")
+		]);
+		console.log(renderTable([
+			"Slug",
+			"Path",
+			"Sessions",
+			"Claude Notes"
+		], tableRows).split("\n").map((l) => "  " + l).join("\n"));
+		console.log();
+	}
+	if (stale.length) {
+		console.log(warn("  Stale projects (path missing, possible new location found):"));
+		for (const r of stale) {
+			console.log(`    ${bold(r.project.slug)}`);
+			console.log(dim(`      Old path:   ${r.project.root_path}`));
+			console.log(chalk.cyan(`      Found at:   ${r.suggestedPath}`));
+			if (r.claudeNotesExists) console.log(chalk.green(`      Notes:      ${r.orphanedNotesDirs.join(", ")}`));
+			if (opts.fix && r.suggestedPath) {
+				const ts = now();
+				const newEncoded = encodeDir(r.suggestedPath);
+				db.prepare("UPDATE projects SET root_path = ?, encoded_dir = ?, updated_at = ? WHERE id = ?").run(r.suggestedPath, newEncoded, ts, r.project.id);
+				console.log(ok(`      Auto-fixed: updated path to ${r.suggestedPath}`));
+			} else if (r.suggestedPath) console.log(dim(`      Fix:        pai project move ${r.project.slug} ${r.suggestedPath}`));
+		}
+		console.log();
+	}
+	if (dead.length) {
+		console.log(err("  Dead projects (path missing, no match found):"));
+		for (const r of dead) {
+			console.log(`    ${bold(r.project.slug)}   ${dim(r.project.root_path)}`);
+			if (r.claudeNotesExists) console.log(chalk.yellow(`      Notes:  ${r.orphanedNotesDirs.join(", ")}`));
+			if (r.project.session_count === 0 && opts.fix) {
+				db.prepare("UPDATE projects SET status = 'archived', archived_at = ?, updated_at = ? WHERE id = ?").run(now(), now(), r.project.id);
+				console.log(ok("      Auto-fixed: archived (0 sessions, path gone)"));
+			} else console.log(dim(`      Fix:    pai project archive ${r.project.slug}  (or  pai project move ...)`));
+		}
+		console.log();
+	}
+	console.log(dim(`  ${rows.length} total: ${active.length} active, ${stale.length} stale, ${dead.length} dead`));
+	if (!opts.fix && (stale.length > 0 || dead.length > 0)) {
+		console.log();
+		console.log(warn("  Run with --fix to auto-remediate where possible."));
+	}
+}
+
+//#endregion
+//#region src/cli/commands/project/index.ts
+function registerProjectCommands(projectCmd, getDb) {
+	projectCmd.command("add <path>").description("Register a project directory in the PAI registry").option("--slug <slug>", "Override auto-generated slug").option("--type <type>", "Project type: local | central | obsidian-linked | external", "local").option("--display-name <name>", "Human-readable display name").action((rawPath, opts) => {
+		cmdAdd(getDb(), rawPath, opts);
+	});
+	projectCmd.command("list").description("List registered projects").option("--status <status>", "Filter by status: active | archived").option("--tag <tag>", "Filter by tag").option("--type <type>", "Filter by type").action((opts) => {
+		cmdList$2(getDb(), opts);
+	});
+	projectCmd.command("info <slug>").description("Show full details for a project").action((slug) => {
+		cmdInfo$1(getDb(), slug);
+	});
+	projectCmd.command("archive <slug>").description("Archive a project").action((slug) => {
+		cmdArchive(getDb(), slug);
+	});
+	projectCmd.command("unarchive <slug>").description("Restore an archived project to active status").action((slug) => {
+		cmdUnarchive(getDb(), slug);
+	});
+	projectCmd.command("move <slug> <new-path>").description("Update the root path for a project").action((slug, newPath) => {
+		cmdMove(getDb(), slug, newPath);
+	});
+	projectCmd.command("tag <slug> <tags...>").description("Add one or more tags to a project").action((slug, tags) => {
+		cmdTag$1(getDb(), slug, tags);
+	});
+	projectCmd.command("alias <slug> <alias>").description("Register an alternative slug for a project").action((slug, alias) => {
+		cmdAlias(getDb(), slug, alias);
+	});
+	projectCmd.command("edit <slug>").description("Edit project metadata").option("--display-name <name>", "New display name").option("--type <type>", "New type").action((slug, opts) => {
+		cmdEdit(getDb(), slug, opts);
+	});
+	projectCmd.command("cd <identifier>").description("Print the root path for a project (use with: cd $(pai project cd <id>))").action((identifier) => {
+		const project = resolveIdentifier(getDb(), identifier);
+		if (!project) {
+			console.error(`Project not found: ${identifier}`);
+			process.exit(1);
+		}
+		process.stdout.write(project.root_path + "\n");
+	});
+	projectCmd.command("detect [path]").description("Detect which registered project the given path (or CWD) belongs to").option("--json", "Output raw JSON instead of human-readable text").action((pathArg, opts) => {
+		cmdDetect(getDb(), pathArg, opts);
+	});
+	projectCmd.command("health").description("Audit all registered projects: check which paths still exist, find moved/dead projects").option("--fix", "Auto-remediate where possible (update moved paths, archive dead zero-session projects)").option("--json", "Output raw JSON report").option("--status <category>", "Filter output to: active | stale | dead").action((opts) => {
 		cmdHealth$1(getDb(), opts);
 	});
 	projectCmd.command("consolidate <identifier>").description("Consolidate scattered ~/.claude/projects/.../Notes/ directories for a project into its canonical Notes/ location").option("--yes", "Perform consolidation without confirmation prompt").option("--dry-run", "Preview what would be moved without making changes").action((identifier, opts) => {
@@ -740,6 +1145,18 @@ function registerProjectCommands(projectCmd, getDb) {
 	projectCmd.command("go <query>").description("Print the root path for a project by slug, partial name, or fuzzy match.\nDesigned for shell integration: cd $(pai project go <query>)\nOr set a shell alias: alias pcd='cd $(pai project go)'").action((query) => {
 		cmdGo(getDb(), query);
 	});
+	projectCmd.command("name <identifier> <shortname>").description("Give a project a short name for quick access (used by AIBroker to launch sessions)").option("--permission <level>", "Permission level: full | trusted | default (or raw CLI flags)").action((identifier, shortname, opts) => {
+		cmdName(getDb(), identifier, shortname, opts);
+	});
+	projectCmd.command("unname <shortname>").description("Remove a project's short name").action((shortname) => {
+		cmdUnname(getDb(), shortname);
+	});
+	projectCmd.command("names").description("List named projects (your curated shortlist)").option("--json", "Output JSON for AIBroker consumption").action((opts) => {
+		cmdNames(getDb(), opts);
+	});
+	projectCmd.command("config [identifier]").description("View or modify session launch config for a project.\nUse --options to discover available keys and presets.\nUse --defaults to manage global defaults for new sessions.").option("--set <key=value...>", "Set config values (repeatable)", (v, prev) => [...prev, v], []).option("--unset <key...>", "Remove config keys (repeatable, use env.KEY for env vars)", (v, prev) => [...prev, v], []).option("--preset <name>", "Apply a permission preset: full | trusted | default").option("--defaults", "Manage global session defaults instead of a project").option("--options", "List available config keys and presets").option("--json", "Output JSON").option("--reset", "Reset config to empty (inherit global defaults)").action((identifier, opts) => {
+		cmdConfig(getDb(), identifier, opts);
+	});
 }
 
 //#endregion
@@ -754,275 +1171,6 @@ function registerProjectCommands(projectCmd, getDb) {
 *   - type "user":      { type: "user",      message: { role: "user",      content: string | [{ type, text }] } }
 *   - type "assistant": { type: "assistant", message: { role: "assistant", content: [{ type, text }] } }
 */
-const STOP_WORDS = new Set([
-	"the",
-	"a",
-	"an",
-	"is",
-	"are",
-	"was",
-	"were",
-	"be",
-	"been",
-	"being",
-	"have",
-	"has",
-	"had",
-	"do",
-	"does",
-	"did",
-	"will",
-	"would",
-	"could",
-	"should",
-	"may",
-	"might",
-	"can",
-	"shall",
-	"this",
-	"that",
-	"these",
-	"those",
-	"it",
-	"its",
-	"i",
-	"you",
-	"we",
-	"they",
-	"he",
-	"she",
-	"my",
-	"your",
-	"our",
-	"their",
-	"what",
-	"which",
-	"who",
-	"whom",
-	"how",
-	"when",
-	"where",
-	"why",
-	"not",
-	"no",
-	"yes",
-	"just",
-	"also",
-	"very",
-	"really",
-	"about",
-	"after",
-	"before",
-	"from",
-	"into",
-	"with",
-	"without",
-	"for",
-	"and",
-	"or",
-	"but",
-	"if",
-	"then",
-	"else",
-	"so",
-	"because",
-	"as",
-	"at",
-	"by",
-	"in",
-	"on",
-	"of",
-	"to",
-	"up",
-	"out",
-	"off",
-	"over",
-	"under",
-	"more",
-	"most",
-	"some",
-	"any",
-	"all",
-	"each",
-	"every",
-	"both",
-	"few",
-	"many",
-	"much",
-	"other",
-	"another",
-	"such",
-	"only",
-	"own",
-	"same",
-	"than",
-	"too",
-	"let",
-	"me",
-	"us",
-	"ok",
-	"okay",
-	"sure",
-	"please",
-	"thanks",
-	"thank",
-	"here",
-	"there",
-	"now",
-	"well",
-	"like",
-	"want",
-	"need",
-	"know",
-	"think",
-	"see",
-	"look",
-	"make",
-	"get",
-	"go",
-	"come",
-	"take",
-	"use",
-	"find",
-	"give",
-	"tell",
-	"say",
-	"said",
-	"try",
-	"keep",
-	"run",
-	"set",
-	"put",
-	"add",
-	"show",
-	"check",
-	"new",
-	"file",
-	"code",
-	"going",
-	"done",
-	"got",
-	"https",
-	"http",
-	"www",
-	"com",
-	"org",
-	"net",
-	"io",
-	"null",
-	"undefined",
-	"true",
-	"false",
-	"ll",
-	"ve",
-	"re",
-	"don",
-	"thats",
-	"its",
-	"heres",
-	"theres",
-	"youre",
-	"theyre",
-	"didnt",
-	"dont",
-	"doesnt",
-	"havent",
-	"hasnt",
-	"wont",
-	"cant",
-	"shouldnt",
-	"wouldnt",
-	"couldnt",
-	"isnt",
-	"arent",
-	"wasnt",
-	"werent",
-	"never",
-	"ever",
-	"still",
-	"already",
-	"yet",
-	"back",
-	"away",
-	"down",
-	"right",
-	"left",
-	"next",
-	"last",
-	"first",
-	"second",
-	"third",
-	"one",
-	"two",
-	"three",
-	"four",
-	"five",
-	"six",
-	"seven",
-	"eight",
-	"nine",
-	"ten",
-	"time",
-	"way",
-	"thing",
-	"something",
-	"anything",
-	"nothing",
-	"everything",
-	"someone",
-	"anyone",
-	"everyone",
-	"then",
-	"again",
-	"once",
-	"twice",
-	"since",
-	"while",
-	"though",
-	"although",
-	"however",
-	"therefore",
-	"thus",
-	"hence",
-	"meanwhile",
-	"moreover",
-	"furthermore",
-	"otherwise",
-	"instead",
-	"anyway",
-	"actually",
-	"basically",
-	"literally",
-	"simply",
-	"exactly",
-	"probably",
-	"possibly",
-	"maybe",
-	"perhaps",
-	"certainly",
-	"definitely",
-	"absolutely",
-	"completely",
-	"totally",
-	"quite",
-	"rather",
-	"fairly",
-	"nearly",
-	"almost",
-	"barely",
-	"hardly",
-	"quickly",
-	"slowly",
-	"easily",
-	"likely",
-	"unlikely",
-	"via",
-	"per",
-	"etc",
-	"ie",
-	"eg",
-	"vs"
-]);
 /**
 * Extract plain text from a parsed JSONL message object.
 */
@@ -1148,7 +1296,7 @@ function generateSlug(messages, opts) {
 }
 
 //#endregion
-//#region src/cli/commands/session.ts
+//#region src/cli/commands/session/helpers.ts
 function getProject$1(db, slug) {
 	return db.prepare("SELECT id, slug, display_name, root_path, encoded_dir FROM projects WHERE slug = ?").get(slug);
 }
@@ -1159,36 +1307,19 @@ function statusColor(status) {
 		default: return chalk.yellow(status);
 	}
 }
-/**
-* Convert a slug to a title-cased display name suitable for filenames.
-*   "memory-engine"     → "Memory Engine"
-*   "slug-generator"    → "Slug Generator"
-*   "session-slug-fix"  → "Session Slug Fix"
-*/
+/** Convert a slug to title-cased display name: "memory-engine" → "Memory Engine" */
 function toTitleCase$1(slug) {
 	return slug.replace(/-/g, " ").replace(/\b\w/g, (c) => c.toUpperCase());
 }
-/**
-* Find the Notes directory for a project.
-*
-* Notes live inside the Claude-managed project directory:
-*   ~/.claude/projects/<encoded_dir>/Notes/
-*/
+/** Notes directory for a project: ~/.claude/projects/<encoded_dir>/Notes/ */
 function getNotesDir(project) {
 	return join(homedir(), ".claude", "projects", project.encoded_dir, "Notes");
 }
-/**
-* Format a session filename from its parts.
-*   number=27, date="2026-02-23", titleSlug="Memory Engine"
-*   → "0027 - 2026-02-23 - Memory Engine.md"
-*/
+/** Format a session filename: number=27, date="2026-02-23" → "0027 - 2026-02-23 - Title.md" */
 function formatFilename(number, date, titleSlug) {
 	return `${String(number).padStart(4, "0")} - ${date} - ${titleSlug}.md`;
 }
-/**
-* Look up a session by project + number OR "latest".
-* Returns the session row or exits with an error.
-*/
+/** Resolve a session by project + number or "latest". Exits on failure. */
 function resolveSession(db, project, numberOrLatest) {
 	let session;
 	if (numberOrLatest === "latest") session = db.prepare("SELECT * FROM sessions WHERE project_id = ? ORDER BY number DESC LIMIT 1").get(project.id);
@@ -1206,7 +1337,20 @@ function resolveSession(db, project, numberOrLatest) {
 	}
 	return session;
 }
-function cmdList(db, projectSlug, opts) {
+function upsertTag(db, tagName) {
+	db.prepare("INSERT OR IGNORE INTO tags (name) VALUES (?)").run(tagName);
+	return db.prepare("SELECT id FROM tags WHERE name = ?").get(tagName).id;
+}
+function getSessionTags(db, sessionId) {
+	return db.prepare(`SELECT t.name FROM tags t
+       JOIN session_tags st ON st.tag_id = t.id
+       WHERE st.session_id = ?
+       ORDER BY t.name`).all(sessionId).map((r) => r.name);
+}
+
+//#endregion
+//#region src/cli/commands/session/commands.ts
+function cmdList$1(db, projectSlug, opts) {
 	const limit = parseInt(opts.limit ?? "20", 10);
 	const params = [];
 	let query = `
@@ -1301,10 +1445,6 @@ function cmdInfo(db, projectSlug, sessionNumber) {
 	if (session.closed_at) console.log(`  ${bold("Closed:")}      ${fmtDate(session.closed_at)}`);
 	console.log();
 }
-/**
-* Rename a session note: updates the database (slug + title), renames the
-* file on disk, and updates the H1 title inside the Markdown file.
-*/
 function cmdRename(db, projectSlug, numberOrLatest, newSlug) {
 	const project = getProject$1(db, projectSlug);
 	if (!project) {
@@ -1357,10 +1497,6 @@ function cmdRename(db, projectSlug, numberOrLatest, newSlug) {
 	console.log(`  ${bold("Title:")} ${titleSlug}`);
 	console.log();
 }
-/**
-* Generate (and optionally apply) a slug for a session by analysing its
-* Claude Code JSONL transcript.
-*/
 function cmdSlug(db, projectSlug, numberOrLatest, opts) {
 	const project = getProject$1(db, projectSlug);
 	if (!project) {
@@ -1388,108 +1524,204 @@ function cmdSlug(db, projectSlug, numberOrLatest, opts) {
 		cmdRename(db, projectSlug, String(session.number), generatedSlug);
 	}
 }
-function upsertTag(db, tagName) {
-	db.prepare("INSERT OR IGNORE INTO tags (name) VALUES (?)").run(tagName);
-	return db.prepare("SELECT id FROM tags WHERE name = ?").get(tagName).id;
-}
-function getSessionTags(db, sessionId) {
-	return db.prepare(`SELECT t.name FROM tags t
-       JOIN session_tags st ON st.tag_id = t.id
-       WHERE st.session_id = ?
-       ORDER BY t.name`).all(sessionId).map((r) => r.name);
-}
-/**
-* Set or show tags on a session.
-*
-* With no tags supplied, prints the current tags.
-* Tags can be supplied as separate args or as a single comma-separated string.
-*   pai session tag 20-webseiten 81           — show current tags
-*   pai session tag 20-webseiten 81 docker migration server
-*   pai session tag 20-webseiten 81 docker,migration,server
-*/
 function cmdTag(db, projectSlug, sessionNumber, rawTags) {
 	const project = getProject$1(db, projectSlug);
 	if (!project) {
 		console.error(err(`Project not found: ${projectSlug}`));
 		process.exit(1);
 	}
-	const session = resolveSession(db, project, sessionNumber);
-	if (rawTags.length === 0) {
-		const current = getSessionTags(db, session.id);
-		console.log();
-		if (current.length === 0) console.log(dim(`  Session #${session.number} has no tags.`));
-		else console.log(`  ${bold(`Session #${session.number}`)} tags: ${current.map((t) => chalk.cyan(t)).join(", ")}`);
-		console.log();
+	const session = resolveSession(db, project, sessionNumber);
+	if (rawTags.length === 0) {
+		const current = getSessionTags(db, session.id);
+		console.log();
+		if (current.length === 0) console.log(dim(`  Session #${session.number} has no tags.`));
+		else console.log(`  ${bold(`Session #${session.number}`)} tags: ${current.map((t) => chalk.cyan(t)).join(", ")}`);
+		console.log();
+		return;
+	}
+	const tags = rawTags.flatMap((t) => t.split(",")).map((t) => t.trim().toLowerCase()).filter((t) => t.length > 0);
+	if (tags.length === 0) {
+		console.log(warn("No valid tags provided."));
+		return;
+	}
+	const added = [];
+	const skipped = [];
+	for (const tagName of tags) {
+		const tagId = upsertTag(db, tagName);
+		if (db.prepare("SELECT 1 FROM session_tags WHERE session_id = ? AND tag_id = ?").get(session.id, tagId)) skipped.push(tagName);
+		else {
+			db.prepare("INSERT INTO session_tags (session_id, tag_id) VALUES (?, ?)").run(session.id, tagId);
+			added.push(tagName);
+		}
+	}
+	console.log();
+	if (added.length) console.log(ok(`  Tagged session #${session.number}: ${added.map((t) => chalk.cyan(t)).join(", ")}`));
+	if (skipped.length) console.log(dim(`  Already present: ${skipped.join(", ")}`));
+	const allTags = getSessionTags(db, session.id);
+	console.log(`  ${bold("All tags:")} ${allTags.map((t) => chalk.cyan(t)).join(", ")}`);
+	console.log();
+}
+function cmdRoute(db, projectSlug, sessionNumber, targetProjectSlug, opts) {
+	const project = getProject$1(db, projectSlug);
+	if (!project) {
+		console.error(err(`Project not found: ${projectSlug}`));
+		process.exit(1);
+	}
+	const session = resolveSession(db, project, sessionNumber);
+	const targetProject = db.prepare("SELECT id, slug, display_name FROM projects WHERE slug = ?").get(targetProjectSlug);
+	if (!targetProject) {
+		console.error(err(`Target project not found: ${targetProjectSlug}`));
+		process.exit(1);
+	}
+	const validTypes = [
+		"related",
+		"follow-up",
+		"reference"
+	];
+	const linkType = opts.type ?? "related";
+	if (!validTypes.includes(linkType)) {
+		console.error(err(`Invalid link type "${linkType}". Valid: ${validTypes.join(", ")}`));
+		process.exit(1);
+	}
+	try {
+		db.prepare(`INSERT INTO links (session_id, target_project_id, link_type, created_at)
+       VALUES (?, ?, ?, ?)`).run(session.id, targetProject.id, linkType, Date.now());
+	} catch {
+		console.log(warn(`  Link already exists: session #${session.number} → ${targetProjectSlug}`));
+		return;
+	}
+	console.log();
+	console.log(ok(`  Linked session #${session.number} (${project.slug}) → ${targetProject.display_name} (${targetProjectSlug})`));
+	console.log(dim(`  Link type: ${linkType}`));
+	console.log();
+}
+function cmdActive(db, opts) {
+	const minutes = parseInt(opts.minutes ?? "60", 10);
+	const cutoff = Date.now() - minutes * 60 * 1e3;
+	const claudeProjectsDir = join(homedir(), ".claude", "projects");
+	if (!existsSync(claudeProjectsDir)) {
+		console.log(err("Claude projects directory not found."));
+		return;
+	}
+	const active = [];
+	const entries = readdirSync(claudeProjectsDir);
+	for (const entry of entries) {
+		const projectDir = join(claudeProjectsDir, entry);
+		try {
+			if (!statSync(projectDir).isDirectory()) continue;
+		} catch {
+			continue;
+		}
+		let latestJsonl = null;
+		let latestMtime = 0;
+		try {
+			for (const file of readdirSync(projectDir)) {
+				if (!file.endsWith(".jsonl")) continue;
+				const filePath = join(projectDir, file);
+				try {
+					const mtime = statSync(filePath).mtimeMs;
+					if (mtime > latestMtime) {
+						latestMtime = mtime;
+						latestJsonl = filePath;
+					}
+				} catch {
+					continue;
+				}
+			}
+		} catch {
+			continue;
+		}
+		if (!latestJsonl || latestMtime < cutoff) continue;
+		const project = db.prepare("SELECT slug, display_name, root_path FROM projects WHERE encoded_dir = ?").get(entry);
+		active.push({
+			slug: project?.slug ?? entry,
+			displayName: project?.display_name ?? project?.slug ?? entry,
+			rootPath: project?.root_path ?? "",
+			encodedDir: entry,
+			lastModified: new Date(latestMtime),
+			jsonlFile: latestJsonl
+		});
+	}
+	active.sort((a, b) => b.lastModified.getTime() - a.lastModified.getTime());
+	const seen = /* @__PURE__ */ new Set();
+	const deduped = active.filter((a) => {
+		const key = a.slug.replace(/-\d+$/, "");
+		if (seen.has(key)) return false;
+		seen.add(key);
+		return true;
+	});
+	if (opts.json) {
+		console.log(JSON.stringify(deduped.map((a) => ({
+			slug: a.slug,
+			display_name: a.displayName,
+			root_path: a.rootPath,
+			last_modified: a.lastModified.toISOString()
+		})), null, 2));
 		return;
 	}
-	const tags = rawTags.flatMap((t) => t.split(",")).map((t) => t.trim().toLowerCase()).filter((t) => t.length > 0);
-	if (tags.length === 0) {
-		console.log(warn("No valid tags provided."));
+	if (deduped.length === 0) {
+		console.log(dim(`No active sessions in the last ${minutes} minutes.`));
 		return;
 	}
-	const added = [];
-	const skipped = [];
-	for (const tagName of tags) {
-		const tagId = upsertTag(db, tagName);
-		if (db.prepare("SELECT 1 FROM session_tags WHERE session_id = ? AND tag_id = ?").get(session.id, tagId)) skipped.push(tagName);
-		else {
-			db.prepare("INSERT INTO session_tags (session_id, tag_id) VALUES (?, ?)").run(session.id, tagId);
-			added.push(tagName);
-		}
-	}
-	console.log();
-	if (added.length) console.log(ok(`  Tagged session #${session.number}: ${added.map((t) => chalk.cyan(t)).join(", ")}`));
-	if (skipped.length) console.log(dim(`  Already present: ${skipped.join(", ")}`));
-	const allTags = getSessionTags(db, session.id);
-	console.log(`  ${bold("All tags:")} ${allTags.map((t) => chalk.cyan(t)).join(", ")}`);
+	console.log(header(`Currently Active Sessions`) + dim(` (modified in last ${minutes}min)`));
 	console.log();
+	const rows = deduped.map((a) => {
+		const time = a.lastModified.toTimeString().slice(0, 5);
+		const dirName = a.rootPath ? a.rootPath.replace(homedir(), "~").split("/").pop() ?? a.slug : a.slug;
+		return [
+			chalk.cyan(dirName),
+			dim(a.slug),
+			chalk.green(time)
+		];
+	});
+	console.log(renderTable([
+		"Directory",
+		"Project",
+		"Last Active"
+	], rows));
 }
-/**
-* Create a cross-reference link from a session to a target project.
-*
-*   pai session route <project-slug> <session-number> <target-project>
-*   pai session route <project-slug> <session-number> <target-project> --type follow-up
-*/
-function cmdRoute(db, projectSlug, sessionNumber, targetProjectSlug, opts) {
-	const project = getProject$1(db, projectSlug);
-	if (!project) {
-		console.error(err(`Project not found: ${projectSlug}`));
-		process.exit(1);
-	}
-	const session = resolveSession(db, project, sessionNumber);
-	const targetProject = db.prepare("SELECT id, slug, display_name FROM projects WHERE slug = ?").get(targetProjectSlug);
-	if (!targetProject) {
-		console.error(err(`Target project not found: ${targetProjectSlug}`));
-		process.exit(1);
-	}
-	const validTypes = [
-		"related",
-		"follow-up",
-		"reference"
-	];
-	const linkType = opts.type ?? "related";
-	if (!validTypes.includes(linkType)) {
-		console.error(err(`Invalid link type "${linkType}". Valid: ${validTypes.join(", ")}`));
-		process.exit(1);
+async function cmdAutoRoute(opts) {
+	const { autoRoute, formatAutoRoute, formatAutoRouteJson } = await import("../auto-route-C-DrW6BL.mjs");
+	const { openRegistry } = await import("../db-BtuN768f.mjs").then((n) => n.t);
+	const { createStorageBackend } = await import("../factory-Ygqe_bVZ.mjs").then((n) => n.n);
+	const { loadConfig } = await import("../config-BuhHWyOK.mjs").then((n) => n.r);
+	const config = loadConfig();
+	const registryDb = openRegistry();
+	const federation = await createStorageBackend(config);
+	const targetCwd = opts.cwd ?? process.cwd();
+	const result = await autoRoute(registryDb, federation, targetCwd, opts.context);
+	if (!result) {
+		console.log();
+		console.log(warn("  No project match found for: " + targetCwd));
+		console.log();
+		console.log(dim("  Tried: path match, PAI.md marker walk") + (opts.context ? dim(", topic detection") : ""));
+		console.log();
+		console.log(dim("  Run 'pai project add .' to register this directory."));
+		console.log();
+		return;
 	}
-	try {
-		db.prepare(`INSERT INTO links (session_id, target_project_id, link_type, created_at)
-       VALUES (?, ?, ?, ?)`).run(session.id, targetProject.id, linkType, Date.now());
-	} catch {
-		console.log(warn(`  Link already exists: session #${session.number} → ${targetProjectSlug}`));
+	if (opts.json) {
+		console.log(formatAutoRouteJson(result));
 		return;
 	}
 	console.log();
-	console.log(ok(`  Linked session #${session.number} (${project.slug}) → ${targetProject.display_name} (${targetProjectSlug})`));
-	console.log(dim(`  Link type: ${linkType}`));
+	console.log(header("  PAI Auto-Route"));
+	console.log();
+	console.log(`  ${bold("Project:")}     ${result.display_name}`);
+	console.log(`  ${bold("Slug:")}        ${result.slug}`);
+	console.log(`  ${bold("Root path:")}   ${result.root_path}`);
+	console.log(`  ${bold("Method:")}      ${result.method}`);
+	console.log(`  ${bold("Confidence:")}  ${(result.confidence * 100).toFixed(0)}%`);
+	console.log();
+	console.log(ok("  Routed to: ") + bold(result.slug));
 	console.log();
 }
+
+//#endregion
+//#region src/cli/commands/session/checkpoint.ts
 /**
-* Find the Notes directory for the current working directory by scanning
-* ~/.claude/projects/ for a matching encoded-dir entry.
-*
-* Returns the Notes dir path if found, or null if the CWD has no Claude
-* project directory yet.
+* Session checkpoint command — appends a timestamped block to the active
+* session note. Designed for use in hooks; fast, silent, rate-limited.
 */
 function findNotesDirForCwd() {
 	const cwd = process.cwd();
@@ -1519,9 +1751,6 @@ function findNotesDirForCwd() {
 	const notesDir = join(claudeProjectsDir, encodedDir, "Notes");
 	return existsSync(notesDir) ? notesDir : null;
 }
-/**
-* Find the most recently modified .md file in a directory.
-*/
 function findLatestNoteFile(notesDir) {
 	let entries;
 	try {
@@ -1545,10 +1774,6 @@ function findLatestNoteFile(notesDir) {
 	}
 	return latestPath;
 }
-/**
-* Rate-limit guard: returns true if the last checkpoint was written less
-* than `minGapSeconds` ago, using a temp file keyed to the notes directory.
-*/
 function checkpointTooRecent(notesDir, minGapSeconds) {
 	const safeKey = notesDir.replace(/[^a-zA-Z0-9]/g, "-").slice(-80);
 	const tmpFile = join(tmpdir(), `pai-checkpoint-${safeKey}`);
@@ -1560,9 +1785,6 @@ function checkpointTooRecent(notesDir, minGapSeconds) {
 		return false;
 	}
 }
-/**
-* Touch the rate-limit sentinel file.
-*/
 function touchCheckpointSentinel(notesDir) {
 	const safeKey = notesDir.replace(/[^a-zA-Z0-9]/g, "-").slice(-80);
 	const tmpFile = join(tmpdir(), `pai-checkpoint-${safeKey}`);
@@ -1570,12 +1792,6 @@ function touchCheckpointSentinel(notesDir) {
 		writeFileSync(tmpFile, String(Date.now()), "utf8");
 	} catch {}
 }
-/**
-* Append a timestamped checkpoint block to the active session note.
-*
-* Designed to be called from Claude Code hooks (PostToolUse,
-* UserPromptSubmit).  Fast, silent, exit 0 on success or skip.
-*/
 function cmdCheckpoint(message, opts) {
 	const minGapSeconds = parseInt(opts.minGap ?? "300", 10);
 	const notesDir = findNotesDirForCwd();
@@ -1597,19 +1813,15 @@ function cmdCheckpoint(message, opts) {
 	touchCheckpointSentinel(notesDir);
 	process.exit(0);
 }
-/**
-* TODO candidate locations searched in priority order (mirrors toolProjectTodo).
-*/
+
+//#endregion
+//#region src/cli/commands/session/handover.ts
 const HANDOVER_TODO_LOCATIONS = [
 	"Notes/TODO.md",
 	".claude/Notes/TODO.md",
 	"tasks/todo.md",
 	"TODO.md"
 ];
-/**
-* Find the TODO.md for a given project root path.
-* Returns { path, content } for the first location that exists, or null.
-*/
 function findProjectTodo(rootPath) {
 	for (const rel of HANDOVER_TODO_LOCATIONS) {
 		const full = join(rootPath, rel);
@@ -1622,11 +1834,6 @@ function findProjectTodo(rootPath) {
 	}
 	return null;
 }
-/**
-* Strip any existing `## Continue` section (up to but not including the
-* first `---` separator or next `##` heading that follows it).
-* Returns the content with that section removed.
-*/
 function stripContinueSection(content) {
 	const lines = content.split("\n");
 	const startIdx = lines.findIndex((l) => l.trim() === "## Continue");
@@ -1646,18 +1853,10 @@ function stripContinueSection(content) {
 	while (after.length > 0 && after[0].trim() === "") after.shift();
 	return [...before, ...after].join("\n");
 }
-/**
-* Write (or overwrite) the `## Continue` section at the TOP of the TODO file.
-*
-*   pai session handover [project-slug] [session-id|"latest"]
-*
-* Called from hooks (session-stop, pre-compact) with project-slug + "latest".
-* Falls back to auto-detecting the project from cwd when no slug is supplied.
-*/
 function cmdHandover(db, projectSlug, numberOrLatest) {
 	let project;
 	if (projectSlug) {
-		project = getProject$1(db, projectSlug);
+		project = db.prepare("SELECT id, slug, display_name, root_path, encoded_dir FROM projects WHERE slug = ?").get(projectSlug);
 		if (!project) process.exit(0);
 	} else {
 		const cwd = process.cwd();
@@ -1710,143 +1909,25 @@ function cmdHandover(db, projectSlug, numberOrLatest) {
 		"",
 		"---",
 		""
-	].join("\n") + stripContinueSection(existingContent).trimStart();
-	const tmpPath = `${todoPath}.handover.tmp`;
-	try {
-		writeFileSync(tmpPath, newContent, "utf8");
-		renameSync(tmpPath, todoPath);
-	} catch {
-		try {
-			if (existsSync(tmpPath)) renameSync(tmpPath, `${tmpPath}.dead`);
-		} catch {}
-		process.exit(0);
-	}
-	process.exit(0);
-}
-function cmdActive(db, opts) {
-	const minutes = parseInt(opts.minutes ?? "60", 10);
-	const cutoff = Date.now() - minutes * 60 * 1e3;
-	const claudeProjectsDir = join(homedir(), ".claude", "projects");
-	if (!existsSync(claudeProjectsDir)) {
-		console.log(err("Claude projects directory not found."));
-		return;
-	}
-	const active = [];
-	const entries = readdirSync(claudeProjectsDir);
-	for (const entry of entries) {
-		const projectDir = join(claudeProjectsDir, entry);
-		try {
-			if (!statSync(projectDir).isDirectory()) continue;
-		} catch {
-			continue;
-		}
-		let latestJsonl = null;
-		let latestMtime = 0;
-		try {
-			for (const file of readdirSync(projectDir)) {
-				if (!file.endsWith(".jsonl")) continue;
-				const filePath = join(projectDir, file);
-				try {
-					const mtime = statSync(filePath).mtimeMs;
-					if (mtime > latestMtime) {
-						latestMtime = mtime;
-						latestJsonl = filePath;
-					}
-				} catch {
-					continue;
-				}
-			}
-		} catch {
-			continue;
-		}
-		if (!latestJsonl || latestMtime < cutoff) continue;
-		const project = db.prepare("SELECT slug, display_name, root_path FROM projects WHERE encoded_dir = ?").get(entry);
-		active.push({
-			slug: project?.slug ?? entry,
-			displayName: project?.display_name ?? project?.slug ?? entry,
-			rootPath: project?.root_path ?? "",
-			encodedDir: entry,
-			lastModified: new Date(latestMtime),
-			jsonlFile: latestJsonl
-		});
-	}
-	active.sort((a, b) => b.lastModified.getTime() - a.lastModified.getTime());
-	const seen = /* @__PURE__ */ new Set();
-	const deduped = active.filter((a) => {
-		const key = a.slug.replace(/-\d+$/, "");
-		if (seen.has(key)) return false;
-		seen.add(key);
-		return true;
-	});
-	if (opts.json) {
-		console.log(JSON.stringify(deduped.map((a) => ({
-			slug: a.slug,
-			display_name: a.displayName,
-			root_path: a.rootPath,
-			last_modified: a.lastModified.toISOString()
-		})), null, 2));
-		return;
-	}
-	if (deduped.length === 0) {
-		console.log(dim(`No active sessions in the last ${minutes} minutes.`));
-		return;
-	}
-	console.log(header(`Currently Active Sessions`) + dim(` (modified in last ${minutes}min)`));
-	console.log();
-	const rows = deduped.map((a) => {
-		const time = a.lastModified.toTimeString().slice(0, 5);
-		const dirName = a.rootPath ? a.rootPath.replace(homedir(), "~").split("/").pop() ?? a.slug : a.slug;
-		return [
-			chalk.cyan(dirName),
-			dim(a.slug),
-			chalk.green(time)
-		];
-	});
-	console.log(renderTable([
-		"Directory",
-		"Project",
-		"Last Active"
-	], rows));
-}
-async function cmdAutoRoute(opts) {
-	const { autoRoute, formatAutoRoute, formatAutoRouteJson } = await import("../auto-route-BG6I_4B1.mjs");
-	const { openRegistry } = await import("../db-4lSqLFb8.mjs").then((n) => n.t);
-	const { createStorageBackend } = await import("../factory-Bzcy70G9.mjs").then((n) => n.n);
-	const { loadConfig } = await import("../config-Cf92lGX_.mjs").then((n) => n.r);
-	const config = loadConfig();
-	const registryDb = openRegistry();
-	const federation = await createStorageBackend(config);
-	const targetCwd = opts.cwd ?? process.cwd();
-	const result = await autoRoute(registryDb, federation, targetCwd, opts.context);
-	if (!result) {
-		console.log();
-		console.log(warn("  No project match found for: " + targetCwd));
-		console.log();
-		console.log(dim("  Tried: path match, PAI.md marker walk") + (opts.context ? dim(", topic detection") : ""));
-		console.log();
-		console.log(dim("  Run 'pai project add .' to register this directory."));
-		console.log();
-		return;
-	}
-	if (opts.json) {
-		console.log(formatAutoRouteJson(result));
-		return;
+	].join("\n") + stripContinueSection(existingContent).trimStart();
+	const tmpPath = `${todoPath}.handover.tmp`;
+	try {
+		writeFileSync(tmpPath, newContent, "utf8");
+		renameSync(tmpPath, todoPath);
+	} catch {
+		try {
+			if (existsSync(tmpPath)) renameSync(tmpPath, `${tmpPath}.dead`);
+		} catch {}
+		process.exit(0);
 	}
-	console.log();
-	console.log(header("  PAI Auto-Route"));
-	console.log();
-	console.log(`  ${bold("Project:")}     ${result.display_name}`);
-	console.log(`  ${bold("Slug:")}        ${result.slug}`);
-	console.log(`  ${bold("Root path:")}   ${result.root_path}`);
-	console.log(`  ${bold("Method:")}      ${result.method}`);
-	console.log(`  ${bold("Confidence:")}  ${(result.confidence * 100).toFixed(0)}%`);
-	console.log();
-	console.log(ok("  Routed to: ") + bold(result.slug));
-	console.log();
+	process.exit(0);
 }
+
+//#endregion
+//#region src/cli/commands/session/index.ts
 function registerSessionCommands(sessionCmd, getDb) {
 	sessionCmd.command("list [project-slug]").description("List sessions, optionally filtered to a single project").option("--limit <n>", "Maximum number of sessions to show", "20").option("--status <status>", "Filter by status: open | completed | compacted").action((projectSlug, opts) => {
-		cmdList(getDb(), projectSlug, opts);
+		cmdList$1(getDb(), projectSlug, opts);
 	});
 	sessionCmd.command("info <project-slug> <number>").description("Show full details for a specific session").action((projectSlug, number) => {
 		cmdInfo(getDb(), projectSlug, number);
@@ -1878,7 +1959,7 @@ function registerSessionCommands(sessionCmd, getDb) {
 }
 
 //#endregion
-//#region src/cli/commands/session-cleanup.ts
+//#region src/cli/commands/session-cleanup/types.ts
 const TEMPLATE_INDICATORS = [
 	"<!-- PAI will add completed work here during session -->",
 	"<!-- PAI will add completed work here -->",
@@ -1887,82 +1968,13 @@ const TEMPLATE_INDICATORS = [
 ];
 const MODERN_PATTERN = /^(\d{4}) - (\d{4}-\d{2}-\d{2}) - (.+)\.md$/;
 const LEGACY_PATTERN = /^(\d{4})_(\d{4}-\d{2}-\d{2})_(.+)\.md$/;
-function getAllProjects(db) {
-	return db.prepare("SELECT id, slug, display_name, root_path, encoded_dir, claude_notes_dir FROM projects WHERE status = 'active' ORDER BY slug").all();
-}
-function getProject(db, slug) {
-	return db.prepare("SELECT id, slug, display_name, root_path, encoded_dir, claude_notes_dir FROM projects WHERE slug = ?").get(slug);
-}
-function getProjectSessions(db, projectId) {
-	return db.prepare("SELECT * FROM sessions WHERE project_id = ? ORDER BY number ASC").all(projectId);
-}
-/**
-* Find the project-root Notes directory (e.g. {root}/Notes or {root}/.claude/Notes).
-* Returns null if neither exists on disk.
-*/
-function findRootNotesDir(rootPath) {
-	const canonical = join(rootPath, "Notes");
-	if (existsSync(canonical)) return canonical;
-	const alt = join(rootPath, ".claude", "Notes");
-	if (existsSync(alt)) return alt;
-	return null;
-}
-/**
-* Find the Claude Code session notes directory for a project.
-* Falls back to computing the path from encoded_dir if claude_notes_dir is not set.
-* Returns null if the directory does not exist on disk, or if it is identical to
-* rootNotesDir (to avoid processing the same directory twice).
-*/
-function findClaudeNotesDir$1(project, rootNotesDir) {
-	const candidate = project.claude_notes_dir ?? join(homedir(), ".claude", "projects", project.encoded_dir, "Notes");
-	if (!existsSync(candidate)) return null;
-	if (rootNotesDir && candidate === rootNotesDir) return null;
-	return candidate;
-}
-/**
-* Collect up to two distinct Notes/ directories for a project.
-* Returns an array of existing, distinct paths in the order:
-*   1. Root Notes/ (from project root_path)
-*   2. Claude Code Notes/ (from claude_notes_dir or encoded_dir)
-*/
-function findAllNotesDirs(project) {
-	const rootDir = findRootNotesDir(project.root_path);
-	const claudeDir = findClaudeNotesDir$1(project, rootDir);
-	const dirs = [];
-	if (rootDir) dirs.push(rootDir);
-	if (claudeDir) dirs.push(claudeDir);
-	return dirs;
-}
+
+//#endregion
+//#region src/cli/commands/session-cleanup/rename.ts
 /**
-* Determine if a file's content is essentially empty (just the template).
-*
-* A file is template-only if:
-*   - It contains a template placeholder marker AND
-*   - The "Work Done" section has no real content after the placeholder
-*     (i.e., no lines with actual text beyond the placeholder comment itself)
+* Auto-name extraction and string helpers for session-cleanup.
+* Derives a meaningful session title from Markdown content.
 */
-function isTemplateOnly(content) {
-	if (!TEMPLATE_INDICATORS.some((ind) => content.includes(ind))) return false;
-	const lines = content.split("\n");
-	let inWorkDone = false;
-	for (const line of lines) {
-		const trimmed = line.trim();
-		if (trimmed === "## Work Done") {
-			inWorkDone = true;
-			continue;
-		}
-		if (trimmed.startsWith("## ") && inWorkDone) break;
-		if (!inWorkDone) continue;
-		if (!trimmed) continue;
-		if (trimmed.startsWith("<!--") && trimmed.endsWith("-->")) continue;
-		if (trimmed.startsWith("<!--")) continue;
-		if (trimmed === "-->") continue;
-		if (trimmed === "Session completed.") continue;
-		if (trimmed === "#Session" || trimmed === "**Tags:** #Session") continue;
-		return false;
-	}
-	return true;
-}
 const META_PHRASE_PATTERNS = [
 	/session initialized and ready for your instructions/i,
 	/fresh session with no pending tasks/i,
@@ -1996,10 +2008,6 @@ const TITLE_CASE_MINOR_WORDS = new Set([
 	"as",
 	"nor"
 ]);
-/**
-* Strip markdown checkbox syntax, bullets, and inline formatting from a line.
-* Returns the cleaned plain text, or null if the result is too short to be useful.
-*/
 function cleanMarkdownLine(raw) {
 	let s = raw.trim();
 	s = s.replace(/^[-*+]\s+\[[ xX]\]\s*/, "");
@@ -2013,17 +2021,9 @@ function cleanMarkdownLine(raw) {
 	s = s.replace(/\s+/g, " ").trim();
 	return s.length >= 4 ? s : null;
 }
-/**
-* Return true if the line contains only meta-status text that should not
-* be used as a session title.
-*/
 function isMetaPhrase(text) {
 	return META_PHRASE_PATTERNS.some((re) => re.test(text));
 }
-/**
-* Convert a string to Title Case, skipping minor words (articles, prepositions)
-* except as the very first word.
-*/
 function toTitleCase(text) {
 	return text.split(" ").map((word, i) => {
 		const lower = word.toLowerCase();
@@ -2031,11 +2031,6 @@ function toTitleCase(text) {
 		return word.charAt(0).toUpperCase() + word.slice(1);
 	}).join(" ");
 }
-/**
-* Sanitize a string into a valid filename component.
-* Strips chars that don't belong in filenames, collapses spaces, trims to
-* 60 chars at a word boundary, then applies Title Case.
-*/
 function sanitizeName(raw) {
 	let s = raw.replace(/[\/\\:*?"<>|#`]/g, "");
 	s = s.replace(/\s+/g, " ").trim();
@@ -2047,16 +2042,6 @@ function sanitizeName(raw) {
 	s = s.trim();
 	return toTitleCase(s);
 }
-/**
-* Extract a meaningful auto-name from session content.
-*
-* Strategy (in priority order):
-*   1. H2 content sections (## Work Done, ## Summary, etc.):
-*      look at the CONTENT under them for the first real work bullet.
-*   2. Other descriptive H2 headings that aren't structural section names.
-*   3. H1 heading — only if it is not a plain session-number line.
-*   5. Fallback: "Unnamed Session".
-*/
 function extractAutoName(content) {
 	const lines = content.split("\n");
 	const CONTENT_SECTION_HEADINGS = new Set([
@@ -2140,28 +2125,65 @@ function extractAutoName(content) {
 	}
 	return "Unnamed Session";
 }
-/**
-* Format a 4-digit padded session number.
-*/
+/** Format a 4-digit padded session number. */
 function padNum(n) {
 	return String(n).padStart(4, "0");
 }
-/**
-* Given the sessions still alive after deletion, build a renumber map.
-* Returns a Map of oldNumber → newNumber.
-*/
-function buildRenumberMap(survivors) {
-	const map = /* @__PURE__ */ new Map();
-	[...survivors].sort((a, b) => a.number - b.number).forEach((s, idx) => {
-		const newNum = idx + 1;
-		if (s.number !== newNum) map.set(s.number, newNum);
-	});
-	return map;
+
+//#endregion
+//#region src/cli/commands/session-cleanup/scanner.ts
+function getAllProjects(db) {
+	return db.prepare("SELECT id, slug, display_name, root_path, encoded_dir, claude_notes_dir FROM projects WHERE status = 'active' ORDER BY slug").all();
+}
+function getProject(db, slug) {
+	return db.prepare("SELECT id, slug, display_name, root_path, encoded_dir, claude_notes_dir FROM projects WHERE slug = ?").get(slug);
+}
+function getProjectSessions(db, projectId) {
+	return db.prepare("SELECT * FROM sessions WHERE project_id = ? ORDER BY number ASC").all(projectId);
+}
+function findRootNotesDir(rootPath) {
+	const canonical = join(rootPath, "Notes");
+	if (existsSync(canonical)) return canonical;
+	const alt = join(rootPath, ".claude", "Notes");
+	if (existsSync(alt)) return alt;
+	return null;
+}
+function findClaudeNotesDir$1(project, rootNotesDir) {
+	const candidate = project.claude_notes_dir ?? join(homedir(), ".claude", "projects", project.encoded_dir, "Notes");
+	if (!existsSync(candidate)) return null;
+	if (rootNotesDir && candidate === rootNotesDir) return null;
+	return candidate;
+}
+function findAllNotesDirs(project) {
+	const rootDir = findRootNotesDir(project.root_path);
+	const claudeDir = findClaudeNotesDir$1(project, rootDir);
+	const dirs = [];
+	if (rootDir) dirs.push(rootDir);
+	if (claudeDir) dirs.push(claudeDir);
+	return dirs;
+}
+function isTemplateOnly(content) {
+	if (!TEMPLATE_INDICATORS.some((ind) => content.includes(ind))) return false;
+	const lines = content.split("\n");
+	let inWorkDone = false;
+	for (const line of lines) {
+		const trimmed = line.trim();
+		if (trimmed === "## Work Done") {
+			inWorkDone = true;
+			continue;
+		}
+		if (trimmed.startsWith("## ") && inWorkDone) break;
+		if (!inWorkDone) continue;
+		if (!trimmed) continue;
+		if (trimmed.startsWith("<!--") && trimmed.endsWith("-->")) continue;
+		if (trimmed.startsWith("<!--")) continue;
+		if (trimmed === "-->") continue;
+		if (trimmed === "Session completed.") continue;
+		if (trimmed === "#Session" || trimmed === "**Tags:** #Session") continue;
+		return false;
+	}
+	return true;
 }
-/**
-* Scan a single Notes/ directory and return all session candidates found in it.
-* Looks in both the flat top-level and any YYYY/MM/ sub-directories.
-*/
 function scanNotesDir(notesDir, dbByFilename) {
 	const candidates = [];
 	let flatFiles = [];
@@ -2222,48 +2244,117 @@ function scanNotesDir(notesDir, dbByFilename) {
 			if (sizeBytes < 400 || isTemplateOnly(content)) classification = "EMPTY";
 			else if (namepart === "New Session" || namepart === (process.env.USER ?? "") || namepart === "session-started-and-ready-for-your-instructions") classification = "UNNAMED";
 		}
-		const candidate = {
-			session: dbSession,
-			filename,
-			filepath,
-			sizeBytes,
-			classification,
-			date,
-			number: num
-		};
-		if (classification === "UNNAMED" || classification === "LEGACY_FORMAT") candidate.autoName = extractAutoName(content);
-		candidates.push(candidate);
-	}
-	return candidates;
-}
-function analyzeProject(db, project) {
-	const notesDirPaths = findAllNotesDirs(project);
-	if (notesDirPaths.length === 0) return null;
-	const dbSessions = getProjectSessions(db, project.id);
-	const dbByFilename = /* @__PURE__ */ new Map();
-	for (const s of dbSessions) dbByFilename.set(s.filename, s);
-	const notesDirPlans = [];
-	const allSurvivors = [];
-	for (const notesDir of notesDirPaths) {
-		const candidates = scanNotesDir(notesDir, dbByFilename);
-		if (candidates.length === 0) continue;
-		const toDelete = candidates.filter((c) => c.classification === "EMPTY");
-		const toRename = candidates.filter((c) => c.classification === "UNNAMED" || c.classification === "LEGACY_FORMAT");
-		const survivors = candidates.filter((c) => c.classification !== "EMPTY");
-		notesDirPlans.push({
-			notesDir,
-			toDelete,
-			toRename,
-			toMove: survivors
-		});
-		allSurvivors.push(...survivors);
+		const candidate = {
+			session: dbSession,
+			filename,
+			filepath,
+			sizeBytes,
+			classification,
+			date,
+			number: num
+		};
+		if (classification === "UNNAMED" || classification === "LEGACY_FORMAT") candidate.autoName = extractAutoName(content);
+		candidates.push(candidate);
+	}
+	return candidates;
+}
+function buildRenumberMap(survivors) {
+	const map = /* @__PURE__ */ new Map();
+	[...survivors].sort((a, b) => a.number - b.number).forEach((s, idx) => {
+		const newNum = idx + 1;
+		if (s.number !== newNum) map.set(s.number, newNum);
+	});
+	return map;
+}
+function analyzeProject(db, project) {
+	const notesDirPaths = findAllNotesDirs(project);
+	if (notesDirPaths.length === 0) return null;
+	const dbSessions = getProjectSessions(db, project.id);
+	const dbByFilename = /* @__PURE__ */ new Map();
+	for (const s of dbSessions) dbByFilename.set(s.filename, s);
+	const notesDirPlans = [];
+	const allSurvivors = [];
+	for (const notesDir of notesDirPaths) {
+		const candidates = scanNotesDir(notesDir, dbByFilename);
+		if (candidates.length === 0) continue;
+		const toDelete = candidates.filter((c) => c.classification === "EMPTY");
+		const toRename = candidates.filter((c) => c.classification === "UNNAMED" || c.classification === "LEGACY_FORMAT");
+		const survivors = candidates.filter((c) => c.classification !== "EMPTY");
+		notesDirPlans.push({
+			notesDir,
+			toDelete,
+			toRename,
+			toMove: survivors
+		});
+		allSurvivors.push(...survivors);
+	}
+	if (notesDirPlans.length === 0) return null;
+	return {
+		project,
+		notesDirs: notesDirPlans,
+		renumberMap: buildRenumberMap(allSurvivors)
+	};
+}
+
+//#endregion
+//#region src/cli/commands/session-cleanup/executor.ts
+async function countVectorDbPaths(oldPaths) {
+	if (oldPaths.length === 0) return 0;
+	try {
+		const { loadConfig } = await import("../config-BuhHWyOK.mjs").then((n) => n.r);
+		const { PostgresBackend } = await import("../postgres-CKf-EDtS.mjs");
+		const config = loadConfig();
+		if (config.storageBackend !== "postgres") return 0;
+		const pgBackend = new PostgresBackend(config.postgres ?? {});
+		if (await pgBackend.testConnection()) {
+			await pgBackend.close();
+			return 0;
+		}
+		const pool = pgBackend.pool;
+		const placeholders = oldPaths.map((_, i) => `$${i + 1}`).join(", ");
+		const result = await pool.query(`SELECT COUNT(*)::text AS n FROM pai_files WHERE path IN (${placeholders})`, oldPaths);
+		await pgBackend.close();
+		return parseInt(result.rows[0]?.n ?? "0", 10);
+	} catch {
+		return 0;
+	}
+}
+async function updateVectorDbPaths(moves) {
+	if (moves.length === 0) return 0;
+	try {
+		const { loadConfig } = await import("../config-BuhHWyOK.mjs").then((n) => n.r);
+		const { PostgresBackend } = await import("../postgres-CKf-EDtS.mjs");
+		const config = loadConfig();
+		if (config.storageBackend !== "postgres") return 0;
+		const pgBackend = new PostgresBackend(config.postgres ?? {});
+		const connErr = await pgBackend.testConnection();
+		if (connErr) {
+			process.stderr.write(`[session-cleanup] Postgres unavailable (${connErr}). Skipping vector DB path update.\n`);
+			await pgBackend.close();
+			return 0;
+		}
+		const client = await pgBackend.pool.connect();
+		let filesUpdated = 0;
+		try {
+			await client.query("BEGIN", []);
+			for (const { oldPath, newPath } of moves) {
+				const r = await client.query("UPDATE pai_files SET path = $1 WHERE path = $2", [newPath, oldPath]);
+				filesUpdated += r.rowCount ?? 0;
+				await client.query("UPDATE pai_chunks SET path = $1 WHERE path = $2", [newPath, oldPath]);
+			}
+			await client.query("COMMIT", []);
+		} catch (e) {
+			await client.query("ROLLBACK", []);
+			throw e;
+		} finally {
+			client.release();
+		}
+		await pgBackend.close();
+		return filesUpdated;
+	} catch (e) {
+		process.stderr.write(`[session-cleanup] Failed to update vector DB paths: ${e}\n`);
+		return -1;
 	}
-	if (notesDirPlans.length === 0) return null;
-	return {
-		project,
-		notesDirs: notesDirPlans,
-		renumberMap: buildRenumberMap(allSurvivors)
-	};
 }
 async function displayDryRun(plans) {
 	let totalDelete = 0;
@@ -2333,74 +2424,6 @@ async function displayDryRun(plans) {
 	console.log(warn("  This is a dry-run. Add --execute to apply changes."));
 	console.log();
 }
-/**
-* Count how many files in the vector DB match the given old paths.
-* Used for dry-run reporting. Returns 0 if Postgres is unavailable.
-*/
-async function countVectorDbPaths(oldPaths) {
-	if (oldPaths.length === 0) return 0;
-	try {
-		const { loadConfig } = await import("../config-Cf92lGX_.mjs").then((n) => n.r);
-		const { PostgresBackend } = await import("../postgres-FXrHDPcE.mjs");
-		const config = loadConfig();
-		if (config.storageBackend !== "postgres") return 0;
-		const pgBackend = new PostgresBackend(config.postgres ?? {});
-		if (await pgBackend.testConnection()) {
-			await pgBackend.close();
-			return 0;
-		}
-		const pool = pgBackend.pool;
-		const placeholders = oldPaths.map((_, i) => `$${i + 1}`).join(", ");
-		const result = await pool.query(`SELECT COUNT(*)::text AS n FROM pai_files WHERE path IN (${placeholders})`, oldPaths);
-		await pgBackend.close();
-		return parseInt(result.rows[0]?.n ?? "0", 10);
-	} catch {
-		return 0;
-	}
-}
-/**
-* Update file paths in pai_files and pai_chunks for all moved session notes.
-* Returns the number of pai_files rows updated, or -1 on error.
-*
-* Both tables store path directly (no FK between them), so both must be updated.
-*/
-async function updateVectorDbPaths(moves) {
-	if (moves.length === 0) return 0;
-	try {
-		const { loadConfig } = await import("../config-Cf92lGX_.mjs").then((n) => n.r);
-		const { PostgresBackend } = await import("../postgres-FXrHDPcE.mjs");
-		const config = loadConfig();
-		if (config.storageBackend !== "postgres") return 0;
-		const pgBackend = new PostgresBackend(config.postgres ?? {});
-		const connErr = await pgBackend.testConnection();
-		if (connErr) {
-			process.stderr.write(`[session-cleanup] Postgres unavailable (${connErr}). Skipping vector DB path update.\n`);
-			await pgBackend.close();
-			return 0;
-		}
-		const client = await pgBackend.pool.connect();
-		let filesUpdated = 0;
-		try {
-			await client.query("BEGIN", []);
-			for (const { oldPath, newPath } of moves) {
-				const filesResult = await client.query("UPDATE pai_files SET path = $1 WHERE path = $2", [newPath, oldPath]);
-				filesUpdated += filesResult.rowCount ?? 0;
-				await client.query("UPDATE pai_chunks SET path = $1 WHERE path = $2", [newPath, oldPath]);
-			}
-			await client.query("COMMIT", []);
-		} catch (e) {
-			await client.query("ROLLBACK", []);
-			throw e;
-		} finally {
-			client.release();
-		}
-		await pgBackend.close();
-		return filesUpdated;
-	} catch (e) {
-		process.stderr.write(`[session-cleanup] Failed to update vector DB paths: ${e}\n`);
-		return -1;
-	}
-}
 async function executeCleanup(db, plans, skipReindex) {
 	let deleted = 0;
 	let renamed = 0;
@@ -2586,6 +2609,9 @@ async function executeCleanup(db, plans, skipReindex) {
 	}
 	console.log();
 }
+
+//#endregion
+//#region src/cli/commands/session-cleanup/index.ts
 function registerSessionCleanupCommand(sessionCmd, getDb) {
 	sessionCmd.command("cleanup [project-slug]").description("Clean up session notes: delete empties, auto-name unnamed, move into YYYY/MM/ hierarchy, renumber").option("--execute", "Actually perform the cleanup (default is dry-run)").option("--no-renumber", "Skip renumbering sessions after deletions").option("--no-reindex", "Skip triggering memory re-index after moves").action(async (projectSlug, opts) => {
 		const db = getDb();
@@ -2621,45 +2647,9 @@ function registerSessionCleanupCommand(sessionCmd, getDb) {
 }
 
 //#endregion
-//#region src/cli/commands/registry.ts
-/**
-* Recursively find all .md files in a directory, including YYYY/MM subdirectories
-* created by session cleanup. Returns filenames (basename only).
-*/
-function findNoteFiles(dir) {
-	const results = [];
-	if (!existsSync(dir)) return results;
-	for (const entry of readdirSync(dir, { withFileTypes: true })) if (entry.isFile() && entry.name.endsWith(".md")) results.push(entry.name);
-	else if (entry.isDirectory() && /^\d{4}$/.test(entry.name)) {
-		const yearDir = join(dir, entry.name);
-		for (const monthEntry of readdirSync(yearDir, { withFileTypes: true })) if (monthEntry.isDirectory() && /^\d{2}$/.test(monthEntry.name)) {
-			const monthDir = join(yearDir, monthEntry.name);
-			for (const noteEntry of readdirSync(monthDir, { withFileTypes: true })) if (noteEntry.isFile() && noteEntry.name.endsWith(".md")) results.push(noteEntry.name);
-		}
-	}
-	return results;
-}
-const CLAUDE_PROJECTS_DIR = join(homedir(), ".claude", "projects");
-const PAI_CONFIG_DIR = join(homedir(), ".pai");
-const PAI_CONFIG_FILE = join(PAI_CONFIG_DIR, "config.json");
-function loadConfig() {
-	if (!existsSync(PAI_CONFIG_FILE)) return { scan_dirs: [] };
-	try {
-		return JSON.parse(readFileSync(PAI_CONFIG_FILE, "utf8"));
-	} catch {
-		return { scan_dirs: [] };
-	}
-}
-function saveConfig(config) {
-	mkdirSync(PAI_CONFIG_DIR, { recursive: true });
-	writeFileSync(PAI_CONFIG_FILE, JSON.stringify(config, null, 2) + "\n", "utf8");
-}
-function resolveHome(p) {
-	if (p.startsWith("~/")) return join(homedir(), p.slice(2));
-	return resolve(p);
-}
+//#region src/cli/commands/registry/utils.ts
 /**
-* Upsert a project row.  Returns { id, isNew }.
+* Upsert a project row. Returns { id, isNew }.
 *
 * Matching priority:
 *  1. root_path  — most reliable; handles slug collisions
@@ -2709,9 +2699,7 @@ function upsertProject(db, slug, rootPath, encodedDir) {
 		isNew: true
 	};
 }
-/**
-* Upsert a session note.  Returns true if newly inserted.
-*/
+/** Upsert a session note. Returns true if newly inserted. */
 function upsertSession(db, projectId, number, date, slug, title, filename) {
 	if (db.prepare("SELECT id FROM sessions WHERE project_id = ? AND number = ?").get(projectId, number)) return false;
 	const ts = now();
@@ -2720,6 +2708,46 @@ function upsertSession(db, projectId, number, date, slug, title, filename) {
      VALUES (?, ?, ?, ?, ?, ?, 'completed', ?)`).run(projectId, number, date, slug, title, filename, ts);
 	return true;
 }
+
+//#endregion
+//#region src/cli/commands/registry/scan.ts
+/** Registry scan command: walk ~/.claude/projects/ and populate the registry. */
+const CLAUDE_PROJECTS_DIR = join(homedir(), ".claude", "projects");
+const PAI_CONFIG_DIR = join(homedir(), ".pai");
+const PAI_CONFIG_FILE = join(PAI_CONFIG_DIR, "config.json");
+function loadScanConfig() {
+	if (!existsSync(PAI_CONFIG_FILE)) return { scan_dirs: [] };
+	try {
+		return JSON.parse(readFileSync(PAI_CONFIG_FILE, "utf8"));
+	} catch {
+		return { scan_dirs: [] };
+	}
+}
+function saveScanConfig(config) {
+	mkdirSync(PAI_CONFIG_DIR, { recursive: true });
+	writeFileSync(PAI_CONFIG_FILE, JSON.stringify(config, null, 2) + "\n", "utf8");
+}
+function resolveHome(p) {
+	if (p.startsWith("~/")) return join(homedir(), p.slice(2));
+	return resolve(p);
+}
+/**
+* Recursively find all .md files in a directory, including YYYY/MM subdirectories.
+* Returns filenames (basename only).
+*/
+function findNoteFiles(dir) {
+	const results = [];
+	if (!existsSync(dir)) return results;
+	for (const entry of readdirSync(dir, { withFileTypes: true })) if (entry.isFile() && entry.name.endsWith(".md")) results.push(entry.name);
+	else if (entry.isDirectory() && /^\d{4}$/.test(entry.name)) {
+		const yearDir = join(dir, entry.name);
+		for (const monthEntry of readdirSync(yearDir, { withFileTypes: true })) if (monthEntry.isDirectory() && /^\d{2}$/.test(monthEntry.name)) {
+			const monthDir = join(yearDir, monthEntry.name);
+			for (const noteEntry of readdirSync(monthDir, { withFileTypes: true })) if (noteEntry.isFile() && noteEntry.name.endsWith(".md")) results.push(noteEntry.name);
+		}
+	}
+	return results;
+}
 function performScan(db) {
 	const result = {
 		projectsScanned: 0,
@@ -2751,7 +2779,7 @@ function performScan(db) {
 		} catch {}
 		const claudeNotesDir = join(CLAUDE_PROJECTS_DIR, encodedDir, "Notes");
 		if (existsSync(claudeNotesDir)) {
-			if (claudeNotesDir !== join(rootPath, "Notes")) db.prepare("UPDATE projects SET claude_notes_dir = ?, updated_at = ? WHERE id = ?").run(claudeNotesDir, now(), id);
+			if (claudeNotesDir !== join(rootPath, "Notes")) db.prepare("UPDATE projects SET claude_notes_dir = ?, updated_at = ? WHERE id = ?").run(claudeNotesDir, Date.now(), id);
 		}
 		if (!existsSync(claudeNotesDir)) continue;
 		const noteFiles = findNoteFiles(claudeNotesDir);
@@ -2781,7 +2809,7 @@ function performScan(db) {
 			}
 		}
 	}
-	const config = loadConfig();
+	const config = loadScanConfig();
 	if (config.scan_dirs.length) for (const rawDir of config.scan_dirs) {
 		const scanDir = resolveHome(rawDir);
 		if (!existsSync(scanDir)) {
@@ -2859,7 +2887,7 @@ function performScan(db) {
 	return result;
 }
 function cmdScan(db) {
-	const config = loadConfig();
+	const config = loadScanConfig();
 	console.log(dim("Scanning ~/.claude/projects/ ..."));
 	if (config.scan_dirs.length) console.log(dim(`Scanning ${config.scan_dirs.length} extra dir(s): ${config.scan_dirs.join(", ")}`));
 	console.log(dim("Scanning project-root Notes/ directories ..."));
@@ -2880,6 +2908,10 @@ function cmdScan(db) {
 		if (result.skipped.length > 10) console.log(dim(`    ... and ${result.skipped.length - 10} more`));
 	}
 }
+
+//#endregion
+//#region src/cli/commands/registry/migrate.ts
+/** Registry migrate command: import data from ~/.claude/session-registry.json. */
 const SESSION_REGISTRY_PATH = join(homedir(), ".claude", "session-registry.json");
 function cmdMigrate$1(db) {
 	if (!existsSync(SESSION_REGISTRY_PATH)) {
@@ -2936,7 +2968,10 @@ function cmdMigrate$1(db) {
 		if (errors.length > 5) console.log(dim(`    ... and ${errors.length - 5} more`));
 	}
 }
-function cmdStats(db) {
+
+//#endregion
+//#region src/cli/commands/registry/index.ts
+function cmdStats$1(db) {
 	const totalProjects = db.prepare("SELECT COUNT(*) AS n FROM projects").get().n;
 	const activeProjects = db.prepare("SELECT COUNT(*) AS n FROM projects WHERE status = 'active'").get().n;
 	const archivedProjects = db.prepare("SELECT COUNT(*) AS n FROM projects WHERE status = 'archived'").get().n;
@@ -2972,10 +3007,6 @@ function cmdRebuild(db) {
 	console.log(dim("Registry cleared. Re-scanning ..."));
 	cmdScan(db);
 }
-/**
-* Print the project slug whose root_path matches the given filesystem path.
-* Exits 0 on success, 1 if not found.  Output is plain (for use in scripts).
-*/
 function cmdLookup(db, fsPath) {
 	const resolved = resolve(fsPath);
 	const row = db.prepare("SELECT slug FROM projects WHERE root_path = ?").get(resolved);
@@ -2983,9 +3014,9 @@ function cmdLookup(db, fsPath) {
 	process.stdout.write(row.slug + "\n");
 }
 function registerRegistryCommands(registryCmd, getDb) {
-	registryCmd.command("scan").description("Walk ~/.claude/projects/ and configured scan_dirs, upsert all projects").option("--add-dir <path>", "Add a directory to scan_dirs config (immediate children become projects)").option("--remove-dir <path>", "Remove a directory from scan_dirs config").option("--show-dirs", "Show currently configured scan directories").action((opts) => {
+	registryCmd.command("scan").description("Walk ~/.claude/projects/ and configured scan_dirs, upsert all projects").option("--add-dir <path>", "Add a directory to scan_dirs config").option("--remove-dir <path>", "Remove a directory from scan_dirs config").option("--show-dirs", "Show currently configured scan directories").action((opts) => {
 		if (opts.showDirs) {
-			const config = loadConfig();
+			const config = loadScanConfig();
 			if (!config.scan_dirs.length) {
 				console.log(dim("  No extra scan directories configured."));
 				console.log(dim("  Use --add-dir <path> to add one."));
@@ -2996,7 +3027,7 @@ function registerRegistryCommands(registryCmd, getDb) {
 			return;
 		}
 		if (opts.addDir) {
-			const config = loadConfig();
+			const config = loadScanConfig();
 			const resolved = resolveHome(opts.addDir);
 			if (!existsSync(resolved)) {
 				console.error(err(`Directory not found: ${resolved}`));
@@ -3006,18 +3037,18 @@ function registerRegistryCommands(registryCmd, getDb) {
 			if (config.scan_dirs.includes(display) || config.scan_dirs.includes(resolved)) console.log(warn(`Already configured: ${display}`));
 			else {
 				config.scan_dirs.push(display);
-				saveConfig(config);
+				saveScanConfig(config);
 				console.log(ok(`Added scan directory: ${bold(display)}`));
 			}
 		}
 		if (opts.removeDir) {
-			const config = loadConfig();
+			const config = loadScanConfig();
 			const resolved = resolveHome(opts.removeDir);
 			const display = resolved.startsWith(homedir()) ? "~" + resolved.slice(homedir().length) : resolved;
 			const before = config.scan_dirs.length;
 			config.scan_dirs = config.scan_dirs.filter((d) => resolveHome(d) !== resolved);
 			if (config.scan_dirs.length < before) {
-				saveConfig(config);
+				saveScanConfig(config);
 				console.log(ok(`Removed scan directory: ${bold(display)}`));
 			} else console.log(warn(`Not found in config: ${display}`));
 		}
@@ -3027,7 +3058,7 @@ function registerRegistryCommands(registryCmd, getDb) {
 		cmdMigrate$1(getDb());
 	});
 	registryCmd.command("stats").description("Show summary statistics for the registry").action(() => {
-		cmdStats(getDb());
+		cmdStats$1(getDb());
 	});
 	registryCmd.command("rebuild").description("Erase all registry data and rebuild from the filesystem (destructive)").action(() => {
 		cmdRebuild(getDb());
@@ -3038,25 +3069,7 @@ function registerRegistryCommands(registryCmd, getDb) {
 }
 
 //#endregion
-//#region src/cli/commands/memory.ts
-/**
-* CLI commands for the PAI memory engine (Phase 2 / Phase 2.5).
-*
-* Commands:
-*   pai memory index [project-slug]   — index one or all projects
-*   pai memory embed [project-slug]   — generate embeddings for un-embedded chunks
-*   pai memory search <query>         — BM25/semantic/hybrid search across federation.db
-*   pai memory status [project-slug]  — show index stats
-*/
-function tierColor(tier) {
-	switch (tier) {
-		case "evergreen": return chalk.green(tier);
-		case "daily": return chalk.yellow(tier);
-		case "topic": return chalk.blue(tier);
-		case "session": return chalk.dim(tier);
-		default: return tier;
-	}
-}
+//#region src/cli/commands/memory/embed.ts
 async function runEmbed(federation, projectId, projectSlug, batchSize = 50) {
 	const label = projectSlug ? `project ${projectSlug}` : "all projects";
 	console.log(dim(`Generating embeddings for ${label} (this may take a while on first run)...`));
@@ -3066,11 +3079,34 @@ async function runEmbed(federation, projectId, projectSlug, batchSize = 50) {
 	process.stdout.write("\r");
 	console.log(ok(`Done.`) + `  ${bold(String(chunksEmbedded))} chunks embedded`);
 }
-function registerMemoryCommands(memoryCmd, getDb) {
+function registerEmbedCommand(memoryCmd, getDb) {
+	memoryCmd.command("embed [project-slug]").description("Generate embeddings for un-embedded chunks (Phase 2.5)").option("--batch-size <n>", "Chunks to embed per batch", "50").action(async (projectSlug, opts) => {
+		const registryDb = getDb();
+		let federation;
+		try {
+			federation = openFederation();
+		} catch (e) {
+			console.error(err(`Failed to open federation database: ${e}`));
+			process.exit(1);
+		}
+		if (projectSlug) {
+			const project = registryDb.prepare("SELECT id, slug FROM projects WHERE slug = ?").get(projectSlug);
+			if (!project) {
+				console.error(err(`Project not found: ${projectSlug}`));
+				process.exit(1);
+			}
+			await runEmbed(federation, project.id, project.slug, parseInt(opts.batchSize ?? "50", 10));
+		} else await runEmbed(federation, void 0, void 0, parseInt(opts.batchSize ?? "50", 10));
+	});
+}
+
+//#endregion
+//#region src/cli/commands/memory/index-cmd.ts
+function registerIndexCommand(memoryCmd, getDb) {
 	memoryCmd.command("index [project-slug]").description("Index memory files for one project or all projects").option("--all", "Index all active projects (default when no slug given)").option("--embed", "Also generate embeddings for newly indexed chunks (Phase 2.5)").option("--direct", "Skip daemon IPC and run index directly (for debugging)").action(async (projectSlug, opts) => {
 		const registryDb = getDb();
 		if (!opts.direct && !projectSlug) try {
-			await new PaiClient(loadConfig$1().socketPath).triggerIndex();
+			await new PaiClient(loadConfig().socketPath).triggerIndex();
 			console.log(ok("Index triggered in daemon.") + dim("  Check daemon logs for progress."));
 			console.log(dim("  Run `pai daemon logs` to watch progress."));
 			return;
@@ -3101,24 +3137,20 @@ function registerMemoryCommands(memoryCmd, getDb) {
 			if (opts.embed) await runEmbed(federation);
 		}
 	});
-	memoryCmd.command("embed [project-slug]").description("Generate embeddings for un-embedded chunks (Phase 2.5)").option("--batch-size <n>", "Chunks to embed per batch", "50").action(async (projectSlug, opts) => {
-		const registryDb = getDb();
-		let federation;
-		try {
-			federation = openFederation();
-		} catch (e) {
-			console.error(err(`Failed to open federation database: ${e}`));
-			process.exit(1);
-		}
-		if (projectSlug) {
-			const project = registryDb.prepare("SELECT id, slug FROM projects WHERE slug = ?").get(projectSlug);
-			if (!project) {
-				console.error(err(`Project not found: ${projectSlug}`));
-				process.exit(1);
-			}
-			await runEmbed(federation, project.id, project.slug, parseInt(opts.batchSize ?? "50", 10));
-		} else await runEmbed(federation, void 0, void 0, parseInt(opts.batchSize ?? "50", 10));
-	});
+}
+
+//#endregion
+//#region src/cli/commands/memory/search.ts
+function tierColor$1(tier) {
+	switch (tier) {
+		case "evergreen": return chalk.green(tier);
+		case "daily": return chalk.yellow(tier);
+		case "topic": return chalk.blue(tier);
+		case "session": return chalk.dim(tier);
+		default: return tier;
+	}
+}
+function registerSearchCommand(memoryCmd, getDb) {
 	memoryCmd.command("search <query>").description("Search indexed memory (BM25 keyword, semantic, or hybrid)").option("--project <slug>", "Restrict search to a specific project").option("--source <source>", "Restrict to 'memory' or 'notes'").option("--limit <n>", "Maximum results to return").option("--mode <mode>", "Search mode: keyword (default), semantic, hybrid").option("--no-rerank", "Skip cross-encoder reranking (reranking is on by default)").option("--recency <days>", "Apply recency boost: score halves every N days. 0 = off").action(async (query, opts) => {
 		const registryDb = getDb();
 		let federation;
@@ -3128,7 +3160,8 @@ function registerMemoryCommands(memoryCmd, getDb) {
 			console.error(err(`Failed to open federation database: ${e}`));
 			process.exit(1);
 		}
-		const searchConfig = loadConfig$1().search;
+		const config = loadConfig();
+		const searchConfig = config.search;
 		const maxResults = parseInt(opts.limit ?? String(searchConfig.defaultLimit), 10);
 		const mode = opts.mode ?? searchConfig.mode;
 		if (![
@@ -3154,7 +3187,7 @@ function registerMemoryCommands(memoryCmd, getDb) {
 		let results;
 		if (mode === "keyword") results = searchMemory(federation, query, searchOpts);
 		else if (mode === "semantic" || mode === "hybrid") {
-			const backend = await createStorageBackend(loadConfig$1());
+			const backend = await createStorageBackend(config);
 			try {
 				const { generateEmbedding } = await import("../embeddings-DGRAPAYb.mjs").then((n) => n.i);
 				console.log(dim("Generating query embedding..."));
@@ -3205,13 +3238,13 @@ function registerMemoryCommands(memoryCmd, getDb) {
 			return;
 		}
 		if (opts.rerank !== false) {
-			const { rerankResults } = await import("../reranker-D7bRAHi6.mjs").then((n) => n.r);
+			const { rerankResults } = await import("../reranker-CMNZcfVx.mjs").then((n) => n.r);
 			console.log(dim("Reranking with cross-encoder..."));
 			results = await rerankResults(query, results, { topK: maxResults });
 		}
 		const recencyDays = parseInt(opts.recency ?? String(searchConfig.recencyBoostDays), 10);
 		if (recencyDays > 0) {
-			const { applyRecencyBoost } = await import("../search-_oHfguA5.mjs").then((n) => n.o);
+			const { applyRecencyBoost } = await import("../search-DC1qhkKn.mjs").then((n) => n.o);
 			console.log(dim(`Applying recency boost (half-life: ${recencyDays} days)...`));
 			results = applyRecencyBoost(results, recencyDays);
 		}
@@ -3221,7 +3254,7 @@ function registerMemoryCommands(memoryCmd, getDb) {
 		console.log(`\n  ${bold(`Search results for: "${query}"`)}${modeLabel}  ${dim(`(${withSlugs.length} found)`)}\n`);
 		for (const result of withSlugs) {
 			const projectLabel = result.projectSlug ? chalk.cyan(result.projectSlug) : chalk.cyan(String(result.projectId));
-			const tierLabel = tierColor(result.tier);
+			const tierLabel = tierColor$1(result.tier);
 			const scoreLabel = dim(`score: ${result.score.toFixed(4)}`);
 			const locationLabel = dim(`${result.path}:${result.startLine}-${result.endLine}`);
 			console.log(`  ${projectLabel}  ${tierLabel}  ${locationLabel}  ${scoreLabel}`);
@@ -3230,6 +3263,20 @@ function registerMemoryCommands(memoryCmd, getDb) {
 			console.log();
 		}
 	});
+}
+
+//#endregion
+//#region src/cli/commands/memory/stats.ts
+function tierColor(tier) {
+	switch (tier) {
+		case "evergreen": return chalk.green(tier);
+		case "daily": return chalk.yellow(tier);
+		case "topic": return chalk.blue(tier);
+		case "session": return chalk.dim(tier);
+		default: return tier;
+	}
+}
+function registerStatsCommands(memoryCmd, getDb) {
 	memoryCmd.command("status [project-slug]").description("Show memory index statistics").action((projectSlug) => {
 		const registryDb = getDb();
 		let federation;
@@ -3300,7 +3347,7 @@ function registerMemoryCommands(memoryCmd, getDb) {
 		}
 	});
 	memoryCmd.command("settings [key] [value]").description("View or modify search settings in ~/.config/pai/config.json").action((key, value) => {
-		const search = loadConfig$1().search;
+		const search = loadConfig().search;
 		if (!key) {
 			console.log(`\n  ${bold("PAI Memory — Search Settings")}\n`);
 			console.log(`  ${bold("mode:")}             ${search.mode}`);
@@ -3376,6 +3423,15 @@ function registerMemoryCommands(memoryCmd, getDb) {
 	});
 }
 
+//#endregion
+//#region src/cli/commands/memory/index.ts
+function registerMemoryCommands(memoryCmd, getDb) {
+	registerIndexCommand(memoryCmd, getDb);
+	registerEmbedCommand(memoryCmd, getDb);
+	registerSearchCommand(memoryCmd, getDb);
+	registerStatsCommands(memoryCmd, getDb);
+}
+
 //#endregion
 //#region src/cli/commands/mcp.ts
 const CLAUDE_JSON_PATH$1 = join(homedir(), ".claude.json");
@@ -3547,7 +3603,7 @@ function generatePlist(daemonBin) {
 `;
 }
 async function cmdStatus$2() {
-	const client = new PaiClient(loadConfig$1().socketPath);
+	const client = new PaiClient(loadConfig().socketPath);
 	try {
 		const s = await client.status();
 		console.log();
@@ -3737,8 +3793,8 @@ function cmdLogs(opts) {
 }
 function registerDaemonCommands(daemonCmd) {
 	daemonCmd.command("serve").description("Start the PAI daemon in the foreground").action(async () => {
-		const { serve } = await import("../daemon-D9evGlgR.mjs").then((n) => n.t);
-		const { loadConfig: lc, ensureConfigDir } = await import("../config-Cf92lGX_.mjs").then((n) => n.r);
+		const { serve } = await import("../daemon-D3hYb5_C.mjs").then((n) => n.t);
+		const { loadConfig: lc, ensureConfigDir } = await import("../config-BuhHWyOK.mjs").then((n) => n.r);
 		ensureConfigDir();
 		await serve(lc());
 	});
@@ -4103,205 +4159,11 @@ function registerRestoreCommands(program) {
 }
 
 //#endregion
-//#region src/cli/commands/settings-manager.ts
-/**
-* settings-manager — merge-not-overwrite utility for ~/.claude/settings.json
-*
-* Provides safe, idempotent writes to Claude Code's settings.json:
-*   - env vars: added only if the key is absent (never overwrites)
-*   - hooks: appended per hookType, deduplicated by command string
-*   - statusLine: written only if the key is not already present
-*/
-const CLAUDE_DIR = join(homedir(), ".claude");
-const SETTINGS_FILE = join(CLAUDE_DIR, "settings.json");
-function readSettingsJson() {
-	if (!existsSync(SETTINGS_FILE)) return {};
-	try {
-		return JSON.parse(readFileSync(SETTINGS_FILE, "utf-8"));
-	} catch {
-		return {};
-	}
-}
-function writeSettingsJson(data) {
-	if (!existsSync(CLAUDE_DIR)) mkdirSync(CLAUDE_DIR, { recursive: true });
-	writeFileSync(SETTINGS_FILE, JSON.stringify(data, null, 2) + "\n", "utf-8");
-}
-/**
-* Merge env vars — add keys that are absent, never overwrite existing ones.
-*/
-function mergeEnv(settings, incoming, report) {
-	let changed = false;
-	const existing = typeof settings["env"] === "object" && settings["env"] !== null ? settings["env"] : {};
-	for (const [key, value] of Object.entries(incoming)) if (Object.prototype.hasOwnProperty.call(existing, key)) report.push(chalk.dim(`  Skipped: env.${key} already set`));
-	else {
-		existing[key] = value;
-		report.push(chalk.green(`  Added env: ${key}`));
-		changed = true;
-	}
-	settings["env"] = existing;
-	return changed;
-}
-/**
-* Strip file extension from a command basename for extension-agnostic dedup.
-* This ensures that e.g. "context-compression-hook.ts" and
-* "context-compression-hook.mjs" are treated as the same hook.
-*/
-function commandStem(cmd) {
-	return (cmd.split("/").pop() ?? cmd).replace(/\.(mjs|ts|js|sh)$/, "");
-}
-/**
-* Collect every command string already registered for a given hookType.
-* Stores full command, basename, AND extension-stripped stem for flexible
-* matching (handles ${PAI_DIR}/Hooks/foo.sh vs /Users/.../Hooks/foo.sh,
-* and .ts → .mjs migrations).
-*/
-function existingCommandsForHookType(rules) {
-	const cmds = /* @__PURE__ */ new Set();
-	for (const rule of rules) for (const entry of rule.hooks) {
-		cmds.add(entry.command);
-		const base = entry.command.split("/").pop();
-		if (base) cmds.add(base);
-		cmds.add(commandStem(entry.command));
-	}
-	return cmds;
-}
-/**
-* Find and remove an existing rule whose command has the same stem
-* (extension-agnostic) as the incoming command. Returns true if a
-* replacement was made. This handles .ts → .mjs migrations cleanly.
-*/
-function replaceStaleHook(existingRules, incomingStem, incomingCommand, incomingMatcher) {
-	for (let i = 0; i < existingRules.length; i++) {
-		const rule = existingRules[i];
-		for (let j = 0; j < rule.hooks.length; j++) if (commandStem(rule.hooks[j].command) === incomingStem && rule.hooks[j].command !== incomingCommand) {
-			rule.hooks[j].command = incomingCommand;
-			if (incomingMatcher !== void 0) rule.matcher = incomingMatcher;
-			return true;
-		}
-	}
-	return false;
-}
-/**
-* Merge hooks — append entries, deduplicating by command string.
-* Extension-agnostic: a .mjs hook replaces an existing .ts hook with the
-* same stem, ensuring clean .ts → .mjs migrations without duplicates.
-*/
-function mergeHooks(settings, incoming, report) {
-	let changed = false;
-	const hooksSection = typeof settings["hooks"] === "object" && settings["hooks"] !== null ? settings["hooks"] : {};
-	for (const entry of incoming) {
-		const { hookType, matcher, command } = entry;
-		const existingRules = Array.isArray(hooksSection[hookType]) ? hooksSection[hookType] : [];
-		const basename = command.split("/").pop() ?? command;
-		const stem = commandStem(command);
-		const existingCmds = existingCommandsForHookType(existingRules);
-		if (existingCmds.has(command) || existingCmds.has(basename)) {
-			report.push(chalk.dim(`  Skipped: hook ${hookType} → ${basename} already registered`));
-			continue;
-		}
-		if (existingCmds.has(stem)) {
-			if (replaceStaleHook(existingRules, stem, command, matcher)) {
-				hooksSection[hookType] = existingRules;
-				report.push(chalk.yellow(`  Upgraded: hook ${hookType} → ${basename} (replaced stale extension)`));
-				changed = true;
-				continue;
-			}
-		}
-		const newRule = { hooks: [{
-			type: "command",
-			command
-		}] };
-		if (matcher !== void 0) newRule.matcher = matcher;
-		existingRules.push(newRule);
-		hooksSection[hookType] = existingRules;
-		report.push(chalk.green(`  Added hook: ${hookType} → ${basename}`));
-		changed = true;
-	}
-	settings["hooks"] = hooksSection;
-	return changed;
-}
-/**
-* Merge statusLine — write only if the key is not already present.
-*/
-function mergeStatusLine(settings, incoming, report) {
-	if (Object.prototype.hasOwnProperty.call(settings, "statusLine")) {
-		report.push(chalk.dim("  Skipped: statusLine already configured"));
-		return false;
-	}
-	settings["statusLine"] = { ...incoming };
-	report.push(chalk.green("  Added statusLine"));
-	return true;
-}
-/**
-* Merge permissions — append allow/deny entries, deduplicating.
-*/
-function mergePermissions(settings, incoming, report) {
-	let changed = false;
-	const perms = typeof settings["permissions"] === "object" && settings["permissions"] !== null ? settings["permissions"] : {};
-	for (const list of ["allow", "deny"]) {
-		const entries = incoming[list];
-		if (!entries || entries.length === 0) continue;
-		const existing = Array.isArray(perms[list]) ? perms[list] : [];
-		const existingSet = new Set(existing);
-		for (const entry of entries) if (existingSet.has(entry)) report.push(chalk.dim(`  Skipped: permissions.${list} "${entry}" already present`));
-		else {
-			existing.push(entry);
-			existingSet.add(entry);
-			report.push(chalk.green(`  Added permissions.${list}: ${entry}`));
-			changed = true;
-		}
-		perms[list] = existing;
-	}
-	settings["permissions"] = perms;
-	return changed;
-}
-/**
-* Merge flags — set keys only if not already present, never overwrite.
-*/
-function mergeFlags(settings, incoming, report) {
-	let changed = false;
-	for (const [key, value] of Object.entries(incoming)) if (Object.prototype.hasOwnProperty.call(settings, key)) report.push(chalk.dim(`  Skipped: ${key} already set`));
-	else {
-		settings[key] = value;
-		report.push(chalk.green(`  Added flag: ${key}`));
-		changed = true;
-	}
-	return changed;
-}
+//#region src/cli/commands/setup/utils.ts
 /**
-* Merge env vars, hooks, and/or a statusLine entry into ~/.claude/settings.json.
-* Never overwrites existing values — only adds what is missing.
-*
-* Returns { changed, report } where report contains human-readable lines.
+* Shared helpers for the PAI setup wizard: chalk colour shortcuts,
+* readline prompts, config read/write, and filesystem path finders.
 */
-function mergeSettings(opts) {
-	const settings = readSettingsJson();
-	const report = [];
-	let changed = false;
-	if (opts.env !== void 0 && Object.keys(opts.env).length > 0) {
-		if (mergeEnv(settings, opts.env, report)) changed = true;
-	}
-	if (opts.hooks !== void 0 && opts.hooks.length > 0) {
-		if (mergeHooks(settings, opts.hooks, report)) changed = true;
-	}
-	if (opts.statusLine !== void 0) {
-		if (mergeStatusLine(settings, opts.statusLine, report)) changed = true;
-	}
-	if (opts.permissions !== void 0) {
-		if (mergePermissions(settings, opts.permissions, report)) changed = true;
-	}
-	if (opts.flags !== void 0 && Object.keys(opts.flags).length > 0) {
-		if (mergeFlags(settings, opts.flags, report)) changed = true;
-	}
-	if (changed) writeSettingsJson(settings);
-	return {
-		changed,
-		report
-	};
-}
-
-//#endregion
-//#region src/cli/commands/setup.ts
 const c = {
 	bold: (s) => chalk.bold(s),
 	dim: (s) => chalk.dim(s),
@@ -4342,10 +4204,7 @@ async function prompt(rl, question) {
 		});
 	});
 }
-/**
-* Prompt for a numbered menu selection.
-* Returns the 0-based index of the selected option, or defaultIdx if empty input.
-*/
+/** Prompt for a numbered menu selection. Returns 0-based index. */
 async function promptMenu(rl, options, defaultIdx = 0) {
 	for (let i = 0; i < options.length; i++) {
 		const num = chalk.bold(`  ${i + 1}.`);
@@ -4363,9 +4222,7 @@ async function promptMenu(rl, options, defaultIdx = 0) {
 		console.log(c.warn(`Please enter a number between 1 and ${options.length}.`));
 	}
 }
-/**
-* Prompt for a yes/no answer. Returns true for yes.
-*/
+/** Prompt for a yes/no answer. Returns true for yes. */
 async function promptYesNo(rl, question, defaultYes = true) {
 	const hint = defaultYes ? "[Y/n]" : "[y/N]";
 	const answer = await prompt(rl, `  ${question} ${chalk.dim(hint)}: `);
@@ -4409,16 +4266,27 @@ function getDockerDir() {
 		join(homedir(), "dev", "ai", "PAI", "docker"),
 		join("/", "usr", "local", "lib", "node_modules", "@tekmidian", "pai", "docker")
 	];
-	for (const c of candidates) if (existsSync(join(c, "docker-compose.yml"))) return c;
+	for (const candidate of candidates) if (existsSync(join(candidate, "docker-compose.yml"))) return candidate;
 	return join(process.cwd(), "docker");
 }
+async function testPostgresConnection(connectionString) {
+	try {
+		const pgModule = await import("pg");
+		const client = new (pgModule.default ?? pgModule).Client({ connectionString });
+		await client.connect();
+		await client.end();
+		return true;
+	} catch {
+		return false;
+	}
+}
 function getTemplatesDir$1() {
 	const candidates = [
 		join(process.cwd(), "templates"),
 		join(homedir(), "dev", "ai", "PAI", "templates"),
 		join("/", "usr", "local", "lib", "node_modules", "@tekmidian", "pai", "templates")
 	];
-	for (const c of candidates) if (existsSync(join(c, "claude-md.template.md"))) return c;
+	for (const candidate of candidates) if (existsSync(join(candidate, "claude-md.template.md"))) return candidate;
 	return join(process.cwd(), "templates");
 }
 function getHooksDir() {
@@ -4427,12 +4295,12 @@ function getHooksDir() {
 		join(homedir(), "dev", "ai", "PAI", "src", "hooks"),
 		join("/", "usr", "local", "lib", "node_modules", "@tekmidian", "pai", "src", "hooks")
 	];
-	for (const c of candidates) if (existsSync(join(c, "session-stop.sh"))) return c;
+	for (const candidate of candidates) if (existsSync(join(candidate, "session-stop.sh"))) return candidate;
 	return join(process.cwd(), "src", "hooks");
 }
 function getDistHooksDir() {
 	const moduleDir = new URL(".", import.meta.url).pathname;
-	const fromModule = join(moduleDir, "..", "hooks");
+	const fromModule = join(moduleDir, "..", "..", "hooks");
 	const candidates = [
 		fromModule,
 		join(process.cwd(), "dist", "hooks"),
@@ -4448,7 +4316,7 @@ function getStatuslineScript() {
 		join(homedir(), "dev", "ai", "PAI", "statusline-command.sh"),
 		join("/", "usr", "local", "lib", "node_modules", "@tekmidian", "pai", "statusline-command.sh")
 	];
-	for (const c of candidates) if (existsSync(c)) return c;
+	for (const candidate of candidates) if (existsSync(candidate)) return candidate;
 	return null;
 }
 function getTabColorScript() {
@@ -4457,9 +4325,30 @@ function getTabColorScript() {
 		join(homedir(), "dev", "ai", "PAI", "tab-color-command.sh"),
 		join("/", "usr", "local", "lib", "node_modules", "@tekmidian", "pai", "tab-color-command.sh")
 	];
-	for (const c of candidates) if (existsSync(c)) return c;
+	for (const candidate of candidates) if (existsSync(candidate)) return candidate;
 	return null;
 }
+
+//#endregion
+//#region src/cli/commands/setup/steps/01-welcome.ts
+/** Step 1: Welcome banner displayed at the start of the setup wizard. */
+function stepWelcome() {
+	line$1();
+	line$1(chalk.bold.cyan("  ╔════════════════════════════════════════╗"));
+	line$1(chalk.bold.cyan("  ║      PAI Knowledge OS — Setup Wizard   ║"));
+	line$1(chalk.bold.cyan("  ╚════════════════════════════════════════╝"));
+	line$1();
+	line$1("  PAI is a personal knowledge system that indexes your files, generates");
+	line$1("  semantic embeddings for intelligent search, and stores everything in a");
+	line$1("  local database so you can search your knowledge base with natural language.");
+	line$1();
+	line$1(c.dim("  This wizard will guide you through the initial configuration."));
+	line$1(c.dim("  Press Ctrl+C at any time to cancel."));
+}
+
+//#endregion
+//#region src/cli/commands/setup/steps/02-storage.ts
+/** Step 2: Storage backend selection (SQLite or PostgreSQL) and Docker helper. */
 async function startDocker(rl) {
 	const dockerDir = getDockerDir();
 	if (!existsSync(join(dockerDir, "docker-compose.yml"))) {
@@ -4476,49 +4365,19 @@ async function startDocker(rl) {
 			"-d"
 		], {
 			cwd: dockerDir,
-			stdio: "inherit"
-		}).status !== 0) {
-			console.log(c.warn("  Docker compose failed. You can start it manually:"));
-			console.log(c.dim(`    cd ${dockerDir} && docker compose up -d`));
-			return false;
-		}
-		console.log(c.ok("PostgreSQL container started."));
-		return true;
-	} catch (e) {
-		console.log(c.warn(`  Could not run docker compose: ${e}`));
-		return false;
-	}
-}
-async function testPostgresConnection(connectionString) {
-	try {
-		const pgModule = await import("pg");
-		const client = new (pgModule.default ?? pgModule).Client({ connectionString });
-		await client.connect();
-		await client.end();
+			stdio: "inherit"
+		}).status !== 0) {
+			console.log(c.warn("  Docker compose failed. You can start it manually:"));
+			console.log(c.dim(`    cd ${dockerDir} && docker compose up -d`));
+			return false;
+		}
+		console.log(c.ok("PostgreSQL container started."));
 		return true;
-	} catch {
+	} catch (e) {
+		console.log(c.warn(`  Could not run docker compose: ${e}`));
 		return false;
 	}
 }
-/**
-* Step 1: Welcome banner and overview
-*/
-function stepWelcome() {
-	line$1();
-	line$1(chalk.bold.cyan("  ╔════════════════════════════════════════╗"));
-	line$1(chalk.bold.cyan("  ║      PAI Knowledge OS — Setup Wizard  ║"));
-	line$1(chalk.bold.cyan("  ╚════════════════════════════════════════╝"));
-	line$1();
-	line$1("  PAI is a personal knowledge system that indexes your files, generates");
-	line$1("  semantic embeddings for intelligent search, and stores everything in a");
-	line$1("  local database so you can search your knowledge base with natural language.");
-	line$1();
-	line$1(c.dim("  This wizard will guide you through the initial configuration."));
-	line$1(c.dim("  Press Ctrl+C at any time to cancel."));
-}
-/**
-* Step 2: Storage backend selection
-*/
 async function stepStorage(rl) {
 	section("Step 2: Storage Backend");
 	const existing = readConfigRaw();
@@ -4578,20 +4437,15 @@ async function stepStorage(rl) {
 			await new Promise((r) => setTimeout(r, 3e3));
 			const connStr = "postgresql://pai:pai@localhost:5432/pai";
 			console.log(c.dim(`  Testing connection to ${connStr}...`));
-			if (await testPostgresConnection(connStr)) {
-				console.log(c.ok("Connection successful!"));
-				return {
-					storageBackend: "postgres",
-					postgres: { connectionString: connStr }
-				};
-			} else {
+			if (await testPostgresConnection(connStr)) console.log(c.ok("Connection successful!"));
+			else {
 				console.log(c.warn("Connection test failed. The container may still be starting."));
 				console.log(c.dim("  Using default connection string — you can verify with `pai daemon status`."));
-				return {
-					storageBackend: "postgres",
-					postgres: { connectionString: connStr }
-				};
 			}
+			return {
+				storageBackend: "postgres",
+				postgres: { connectionString: connStr }
+			};
 		}
 	} else console.log(c.dim("  Docker not found. Using manual connection string entry."));
 	line$1();
@@ -4622,9 +4476,10 @@ async function stepStorage(rl) {
 		postgres: { connectionString: connStr }
 	};
 }
-/**
-* Step 3: Embedding model selection
-*/
+
+//#endregion
+//#region src/cli/commands/setup/steps/03-embedding.ts
+/** Step 3: Embedding model selection for semantic search. */
 async function stepEmbedding(rl) {
 	section("Step 3: Embedding Model");
 	const existing = readConfigRaw();
@@ -4670,9 +4525,10 @@ async function stepEmbedding(rl) {
 	}
 	return { embeddingModel: selectedModel ?? "none" };
 }
-/**
-* Step 4: Agent configuration — generate ~/.claude/CLAUDE.md from template
-*/
+
+//#endregion
+//#region src/cli/commands/setup/steps/04-claude-md.ts
+/** Step 4: CLAUDE.md generation from PAI template. */
 async function stepClaudeMd(rl) {
 	section("Step 4: Agent Configuration (CLAUDE.md)");
 	line$1();
@@ -4733,9 +4589,10 @@ async function stepClaudeMd(rl) {
 	} else console.log(c.dim("  Personal preferences: " + agentPrefs));
 	return true;
 }
-/**
-* Step 5: PAI skill installation (~/.claude/skills/PAI/SKILL.md)
-*/
+
+//#endregion
+//#region src/cli/commands/setup/steps/05-pai-skill.ts
+/** Step 5: PAI SKILL.md installation to ~/.claude/skills/PAI/. */
 async function stepPaiSkill(rl) {
 	section("Step 5: PAI Skill Installation");
 	line$1();
@@ -4779,9 +4636,10 @@ async function stepPaiSkill(rl) {
 	console.log(c.ok("Installed ~/.claude/skills/PAI/SKILL.md"));
 	return true;
 }
-/**
-* Step 6: AI Steering Rules installation (~/.claude/skills/PAI/AI-STEERING-RULES.md)
-*/
+
+//#endregion
+//#region src/cli/commands/setup/steps/06-steering-rules.ts
+/** Step 6: AI Steering Rules installation to ~/.claude/skills/PAI/. */
 async function stepAiSteeringRules(rl) {
 	section("Step 6: AI Steering Rules");
 	line$1();
@@ -4826,9 +4684,10 @@ async function stepAiSteeringRules(rl) {
 	console.log(c.ok("Installed ~/.claude/skills/PAI/AI-STEERING-RULES.md"));
 	return true;
 }
-/**
-* Step 7: Hook scripts (pre-compact, session-stop, statusline)
-*/
+
+//#endregion
+//#region src/cli/commands/setup/steps/08-hooks.ts
+/** Step 7: Shell lifecycle hooks installation (pre-compact, session-stop, statusline). */
 async function stepHooks(rl) {
 	section("Step 7: Lifecycle Hooks");
 	line$1();
@@ -4872,13 +4731,10 @@ async function stepHooks(rl) {
 	else console.log(c.warn("  tab-color-command.sh not found — skipping tab color."));
 	return anyInstalled;
 }
-/**
-* Step 7b: Install compiled TypeScript hooks (.mjs) to ~/.claude/Hooks/
-*
-* Finds all .mjs files in the package's dist/hooks/ directory and copies them
-* to ~/.claude/Hooks/. Content is compared before copying — identical files are
-* skipped for idempotent re-runs. Each installed file gets chmod 755.
-*/
+
+//#endregion
+//#region src/cli/commands/setup/steps/09-ts-hooks.ts
+/** Step 7b: TypeScript (.mjs) hooks installation to ~/.claude/Hooks/. */
 async function stepTsHooks(rl) {
 	section("Step 7b: TypeScript Hooks Installation");
 	line$1();
@@ -4940,22 +4796,218 @@ async function stepTsHooks(rl) {
 			cleanedCount++;
 		}
 	}
-	line$1();
-	if (copiedCount > 0 || cleanedCount > 0) {
-		const parts = [];
-		if (copiedCount > 0) parts.push(`${copiedCount} hook(s) installed`);
-		if (skippedCount > 0) parts.push(`${skippedCount} unchanged`);
-		if (cleanedCount > 0) parts.push(`${cleanedCount} stale .ts file(s) cleaned up`);
-		console.log(c.ok(parts.join(", ") + "."));
-	} else console.log(c.dim(`  All ${skippedCount} hook(s) already up-to-date.`));
-	return copiedCount > 0 || cleanedCount > 0;
+	line$1();
+	if (copiedCount > 0 || cleanedCount > 0) {
+		const parts = [];
+		if (copiedCount > 0) parts.push(`${copiedCount} hook(s) installed`);
+		if (skippedCount > 0) parts.push(`${skippedCount} unchanged`);
+		if (cleanedCount > 0) parts.push(`${cleanedCount} stale .ts file(s) cleaned up`);
+		console.log(c.ok(parts.join(", ") + "."));
+	} else console.log(c.dim(`  All ${skippedCount} hook(s) already up-to-date.`));
+	return copiedCount > 0 || cleanedCount > 0;
+}
+
+//#endregion
+//#region src/cli/commands/settings-manager.ts
+/**
+* settings-manager — merge-not-overwrite utility for ~/.claude/settings.json
+*
+* Provides safe, idempotent writes to Claude Code's settings.json:
+*   - env vars: added only if the key is absent (never overwrites)
+*   - hooks: appended per hookType, deduplicated by command string
+*   - statusLine: written only if the key is not already present
+*/
+const CLAUDE_DIR = join(homedir(), ".claude");
+const SETTINGS_FILE = join(CLAUDE_DIR, "settings.json");
+function readSettingsJson() {
+	if (!existsSync(SETTINGS_FILE)) return {};
+	try {
+		return JSON.parse(readFileSync(SETTINGS_FILE, "utf-8"));
+	} catch {
+		return {};
+	}
+}
+function writeSettingsJson(data) {
+	if (!existsSync(CLAUDE_DIR)) mkdirSync(CLAUDE_DIR, { recursive: true });
+	writeFileSync(SETTINGS_FILE, JSON.stringify(data, null, 2) + "\n", "utf-8");
+}
+/**
+* Merge env vars — add keys that are absent, never overwrite existing ones.
+*/
+function mergeEnv(settings, incoming, report) {
+	let changed = false;
+	const existing = typeof settings["env"] === "object" && settings["env"] !== null ? settings["env"] : {};
+	for (const [key, value] of Object.entries(incoming)) if (Object.prototype.hasOwnProperty.call(existing, key)) report.push(chalk.dim(`  Skipped: env.${key} already set`));
+	else {
+		existing[key] = value;
+		report.push(chalk.green(`  Added env: ${key}`));
+		changed = true;
+	}
+	settings["env"] = existing;
+	return changed;
+}
+/**
+* Strip file extension from a command basename for extension-agnostic dedup.
+* This ensures that e.g. "context-compression-hook.ts" and
+* "context-compression-hook.mjs" are treated as the same hook.
+*/
+function commandStem(cmd) {
+	return (cmd.split("/").pop() ?? cmd).replace(/\.(mjs|ts|js|sh)$/, "");
+}
+/**
+* Collect every command string already registered for a given hookType.
+* Stores full command, basename, AND extension-stripped stem for flexible
+* matching (handles ${PAI_DIR}/Hooks/foo.sh vs /Users/.../Hooks/foo.sh,
+* and .ts → .mjs migrations).
+*/
+function existingCommandsForHookType(rules) {
+	const cmds = /* @__PURE__ */ new Set();
+	for (const rule of rules) for (const entry of rule.hooks) {
+		cmds.add(entry.command);
+		const base = entry.command.split("/").pop();
+		if (base) cmds.add(base);
+		cmds.add(commandStem(entry.command));
+	}
+	return cmds;
+}
+/**
+* Find and remove an existing rule whose command has the same stem
+* (extension-agnostic) as the incoming command. Returns true if a
+* replacement was made. This handles .ts → .mjs migrations cleanly.
+*/
+function replaceStaleHook(existingRules, incomingStem, incomingCommand, incomingMatcher) {
+	for (let i = 0; i < existingRules.length; i++) {
+		const rule = existingRules[i];
+		for (let j = 0; j < rule.hooks.length; j++) if (commandStem(rule.hooks[j].command) === incomingStem && rule.hooks[j].command !== incomingCommand) {
+			rule.hooks[j].command = incomingCommand;
+			if (incomingMatcher !== void 0) rule.matcher = incomingMatcher;
+			return true;
+		}
+	}
+	return false;
+}
+/**
+* Merge hooks — append entries, deduplicating by command string.
+* Extension-agnostic: a .mjs hook replaces an existing .ts hook with the
+* same stem, ensuring clean .ts → .mjs migrations without duplicates.
+*/
+function mergeHooks(settings, incoming, report) {
+	let changed = false;
+	const hooksSection = typeof settings["hooks"] === "object" && settings["hooks"] !== null ? settings["hooks"] : {};
+	for (const entry of incoming) {
+		const { hookType, matcher, command } = entry;
+		const existingRules = Array.isArray(hooksSection[hookType]) ? hooksSection[hookType] : [];
+		const basename = command.split("/").pop() ?? command;
+		const stem = commandStem(command);
+		const existingCmds = existingCommandsForHookType(existingRules);
+		if (existingCmds.has(command) || existingCmds.has(basename)) {
+			report.push(chalk.dim(`  Skipped: hook ${hookType} → ${basename} already registered`));
+			continue;
+		}
+		if (existingCmds.has(stem)) {
+			if (replaceStaleHook(existingRules, stem, command, matcher)) {
+				hooksSection[hookType] = existingRules;
+				report.push(chalk.yellow(`  Upgraded: hook ${hookType} → ${basename} (replaced stale extension)`));
+				changed = true;
+				continue;
+			}
+		}
+		const newRule = { hooks: [{
+			type: "command",
+			command
+		}] };
+		if (matcher !== void 0) newRule.matcher = matcher;
+		existingRules.push(newRule);
+		hooksSection[hookType] = existingRules;
+		report.push(chalk.green(`  Added hook: ${hookType} → ${basename}`));
+		changed = true;
+	}
+	settings["hooks"] = hooksSection;
+	return changed;
+}
+/**
+* Merge statusLine — write only if the key is not already present.
+*/
+function mergeStatusLine(settings, incoming, report) {
+	if (Object.prototype.hasOwnProperty.call(settings, "statusLine")) {
+		report.push(chalk.dim("  Skipped: statusLine already configured"));
+		return false;
+	}
+	settings["statusLine"] = { ...incoming };
+	report.push(chalk.green("  Added statusLine"));
+	return true;
+}
+/**
+* Merge permissions — append allow/deny entries, deduplicating.
+*/
+function mergePermissions(settings, incoming, report) {
+	let changed = false;
+	const perms = typeof settings["permissions"] === "object" && settings["permissions"] !== null ? settings["permissions"] : {};
+	for (const list of ["allow", "deny"]) {
+		const entries = incoming[list];
+		if (!entries || entries.length === 0) continue;
+		const existing = Array.isArray(perms[list]) ? perms[list] : [];
+		const existingSet = new Set(existing);
+		for (const entry of entries) if (existingSet.has(entry)) report.push(chalk.dim(`  Skipped: permissions.${list} "${entry}" already present`));
+		else {
+			existing.push(entry);
+			existingSet.add(entry);
+			report.push(chalk.green(`  Added permissions.${list}: ${entry}`));
+			changed = true;
+		}
+		perms[list] = existing;
+	}
+	settings["permissions"] = perms;
+	return changed;
+}
+/**
+* Merge flags — set keys only if not already present, never overwrite.
+*/
+function mergeFlags(settings, incoming, report) {
+	let changed = false;
+	for (const [key, value] of Object.entries(incoming)) if (Object.prototype.hasOwnProperty.call(settings, key)) report.push(chalk.dim(`  Skipped: ${key} already set`));
+	else {
+		settings[key] = value;
+		report.push(chalk.green(`  Added flag: ${key}`));
+		changed = true;
+	}
+	return changed;
+}
+/**
+* Merge env vars, hooks, and/or a statusLine entry into ~/.claude/settings.json.
+* Never overwrites existing values — only adds what is missing.
+*
+* Returns { changed, report } where report contains human-readable lines.
+*/
+function mergeSettings(opts) {
+	const settings = readSettingsJson();
+	const report = [];
+	let changed = false;
+	if (opts.env !== void 0 && Object.keys(opts.env).length > 0) {
+		if (mergeEnv(settings, opts.env, report)) changed = true;
+	}
+	if (opts.hooks !== void 0 && opts.hooks.length > 0) {
+		if (mergeHooks(settings, opts.hooks, report)) changed = true;
+	}
+	if (opts.statusLine !== void 0) {
+		if (mergeStatusLine(settings, opts.statusLine, report)) changed = true;
+	}
+	if (opts.permissions !== void 0) {
+		if (mergePermissions(settings, opts.permissions, report)) changed = true;
+	}
+	if (opts.flags !== void 0 && Object.keys(opts.flags).length > 0) {
+		if (mergeFlags(settings, opts.flags, report)) changed = true;
+	}
+	if (changed) writeSettingsJson(settings);
+	return {
+		changed,
+		report
+	};
 }
-/**
-* Step 8b: Prompt for the DA (Digital Assistant) name
-*
-* The name appears in tab titles, session notes, and hook output.
-* Stored in env.DA via settings merge.
-*/
+
+//#endregion
+//#region src/cli/commands/setup/steps/10-settings.ts
+/** Steps 8b and 8: Assistant name prompt and settings.json patch. */
 async function stepDaName(rl) {
 	section("Step 8b: Assistant Name");
 	line$1();
@@ -4967,12 +5019,6 @@ async function stepDaName(rl) {
 	console.log(c.ok(`Assistant name set to: ${daName}`));
 	return daName;
 }
-/**
-* Step 8: Patch ~/.claude/settings.json with PAI hooks, env vars, permissions, and flags
-*
-* Registers all 17 hook entries across 8 event types, adds env vars including DA name,
-* sets the statusline command, adds tool permissions (allow/deny), and sets flags.
-*/
 async function stepSettings(rl, daName) {
 	section("Step 8: Settings Patch");
 	line$1();
@@ -5131,9 +5177,10 @@ async function stepSettings(rl, daName) {
 	if (!result.changed) console.log(c.dim("  Settings already up-to-date. No changes made."));
 	return result.changed;
 }
-/**
-* Step 9: Daemon install (launchd plist)
-*/
+
+//#endregion
+//#region src/cli/commands/setup/steps/11-daemon.ts
+/** Step 9: PAI daemon installation via launchd plist. */
 async function stepDaemon(rl) {
 	section("Step 9: Daemon Install");
 	line$1();
@@ -5158,9 +5205,10 @@ async function stepDaemon(rl) {
 	console.log(c.ok("Daemon installed as com.pai.pai-daemon."));
 	return true;
 }
-/**
-* Step 10: MCP registration in ~/.claude.json
-*/
+
+//#endregion
+//#region src/cli/commands/setup/steps/12-mcp.ts
+/** Step 10: PAI MCP server registration in ~/.claude.json. */
 async function stepMcp(rl) {
 	section("Step 10: MCP Registration");
 	line$1();
@@ -5188,9 +5236,10 @@ async function stepMcp(rl) {
 	console.log(c.ok("PAI MCP server registered in ~/.claude.json."));
 	return true;
 }
-/**
-* Step 11: Directory scanning configuration
-*/
+
+//#endregion
+//#region src/cli/commands/setup/steps/13-directories.ts
+/** Step 11: Directory scanning configuration and registry scan prompt. */
 async function stepDirectories(rl) {
 	section("Step 11: Directories to Index");
 	line$1();
@@ -5211,16 +5260,17 @@ async function stepDirectories(rl) {
 	const runScan = await promptYesNo(rl, "Run `pai registry scan` to auto-detect projects after setup?", false);
 	if (runScan) {
 		line$1();
-		console.log(c.dim("  Registry scan will run after setup completes."));
+		console.log(chalk.dim("  Registry scan will run after setup completes."));
 	} else {
-		console.log(c.dim("  Add projects manually: pai project add <path>"));
-		console.log(c.dim("  Or discover them later: pai registry scan"));
+		console.log(chalk.dim("  Add projects manually: pai project add <path>"));
+		console.log(chalk.dim("  Or discover them later: pai registry scan"));
 	}
 	stepDirectories._runScan = runScan;
 }
-/**
-* Step 12: Initial index
-*/
+
+//#endregion
+//#region src/cli/commands/setup/steps/14-initial-index.ts
+/** Step 12: Initial index — optionally starts the daemon and runs registry scan. */
 async function stepInitialIndex(rl) {
 	section("Step 12: Initial Index");
 	line$1();
@@ -5254,22 +5304,23 @@ async function stepInitialIndex(rl) {
 			console.log(c.warn("Could not run registry scan. Run manually: pai registry scan"));
 		}
 	} else {
-		console.log(c.dim("  Start the daemon later: pai daemon serve"));
-		console.log(c.dim("  Scan projects later: pai registry scan"));
+		console.log(chalk.dim("  Start the daemon later: pai daemon serve"));
+		console.log(chalk.dim("  Scan projects later: pai registry scan"));
 	}
 	else {
-		console.log(c.dim("  Register projects with: pai project add <path>"));
-		console.log(c.dim("  Then index them with: pai memory index --all"));
-		console.log(c.dim("  Or start the daemon: pai daemon serve"));
+		console.log(chalk.dim("  Register projects with: pai project add <path>"));
+		console.log(chalk.dim("  Then index them with: pai memory index --all"));
+		console.log(chalk.dim("  Or start the daemon: pai daemon serve"));
 	}
 }
-/**
-* Step 13: Summary and next steps
-*/
+
+//#endregion
+//#region src/cli/commands/setup/steps/15-verify.ts
+/** Step 13: Setup summary — displays all configuration choices made during setup. */
 function stepSummary(configUpdates, claudeMdGenerated, paiSkillInstalled, aiSteeringRulesInstalled, hooksInstalled, tsHooksInstalled, settingsPatched, daName, daemonInstalled, mcpRegistered) {
 	section("Setup Complete");
 	line$1();
-	console.log(c.ok("PAI Knowledge OS is configured!"));
+	console.log(chalk.green("  PAI Knowledge OS is configured!"));
 	line$1();
 	const backend = configUpdates.storageBackend;
 	const model = configUpdates.embeddingModel;
@@ -5315,11 +5366,14 @@ function stepSummary(configUpdates, claudeMdGenerated, paiSkillInstalled, aiStee
 	console.log(chalk.cyan("    pai --help"));
 	line$1();
 }
+
+//#endregion
+//#region src/cli/commands/setup/index.ts
 async function runSetup() {
 	const rl = createRl();
 	try {
 		if (existsSync(CONFIG_FILE$2)) {
-			const current = loadConfig$1();
+			const current = loadConfig();
 			line$1();
 			console.log(chalk.yellow("  Note: PAI is already configured.") + chalk.dim(" Proceeding will update your existing configuration."));
 			console.log(chalk.dim(`  Config: ${CONFIG_FILE$2}`));
@@ -5327,7 +5381,7 @@ async function runSetup() {
 			line$1();
 			if (!await promptYesNo(rl, "Continue and update configuration?", true)) {
 				rl.close();
-				line$1(c.dim("  Setup cancelled."));
+				line$1(chalk.dim("  Setup cancelled."));
 				line$1();
 				return;
 			}
@@ -5353,7 +5407,7 @@ async function runSetup() {
 		};
 		mergeConfig(allUpdates);
 		line$1();
-		console.log(c.ok("Configuration saved."));
+		console.log(chalk.green("  Configuration saved."));
 		await stepInitialIndex(rl);
 		stepSummary(allUpdates, claudeMdGenerated, paiSkillInstalled, aiSteeringRulesInstalled, hooksInstalled, tsHooksInstalled, settingsPatched, daName, daemonInstalled, mcpRegistered);
 	} finally {
@@ -5367,11 +5421,9 @@ function registerSetupCommand(program) {
 }
 
 //#endregion
-//#region src/obsidian/sync.ts
-/**
-* Find the project-root Notes directory for a project.
-* Checks canonical location first, then .claude/Notes.
-*/
+//#region src/obsidian/sync/symlinks.ts
+/** Symlink management: create, validate, migrate, and clean vault project symlinks. */
+/** Find the project-root Notes directory for a project. */
 function findNotesDir(rootPath) {
 	const canonical = join(rootPath, "Notes");
 	if (existsSync(canonical)) return canonical;
@@ -5381,8 +5433,7 @@ function findNotesDir(rootPath) {
 }
 /**
 * Find the Claude Code session notes directory from the registry-stored value.
-* Returns null if not set or does not exist on disk.
-* Skips the dir if it is identical to the project-root notesDir (avoids double-linking).
+* Returns null if not set, missing on disk, or identical to notesDir.
 */
 function findClaudeNotesDir(claudeNotesDirFromRegistry, notesDir) {
 	if (!claudeNotesDirFromRegistry) return null;
@@ -5390,9 +5441,7 @@ function findClaudeNotesDir(claudeNotesDirFromRegistry, notesDir) {
 	if (notesDir && claudeNotesDirFromRegistry === notesDir) return null;
 	return claudeNotesDirFromRegistry;
 }
-/**
-* Check whether a path exists via lstat (does not follow symlinks).
-*/
+/** Check whether a path exists via lstat (does not follow symlinks). */
 function lstatExists(p) {
 	try {
 		lstatSync(p);
@@ -5401,9 +5450,7 @@ function lstatExists(p) {
 		return false;
 	}
 }
-/**
-* Resolve slug collisions by appending -2, -3, etc.
-*/
+/** Resolve slug collisions by appending -2, -3, etc. */
 function uniqueSlug(base, taken) {
 	if (!taken.has(base)) return base;
 	let n = 2;
@@ -5432,12 +5479,7 @@ function cleanBrokenSymlinks(dir) {
 }
 /**
 * Ensure a sub-symlink inside a project directory is correct.
-*
-* If the symlink already points to the right target, nothing changes.
-* If it points somewhere else, it is removed and recreated.
-* If the path is a non-symlink, it is left alone (data-loss prevention).
-*
-* @returns true if a new symlink was created, false otherwise.
+* Returns true if a new symlink was created, false otherwise.
 */
 function ensureSubSymlink(linkPath, target, errors, label) {
 	if (lstatExists(linkPath)) try {
@@ -5462,14 +5504,8 @@ function ensureSubSymlink(linkPath, target, errors, label) {
 }
 /**
 * Migrate a legacy flat symlink at `slugPath` to a real directory.
-*
-* The old structure was:  {vault}/{slug} → {notesDir}
-* The new structure is:   {vault}/{slug}/            (real dir)
-*                           notes    → {notesDir}
-*                           sessions → {claudeNotesDir}
-*
 * If `slugPath` is already a real directory, this is a no-op.
-* If it is a symlink (legacy), it is removed so `mkdirSync` can create the dir.
+* If it is a symlink (legacy), it is removed so mkdirSync can create the dir.
 */
 function migrateToProjectDir(slugPath, errors, slug) {
 	if (!lstatExists(slugPath)) return true;
@@ -5490,13 +5526,11 @@ function migrateToProjectDir(slugPath, errors, slug) {
 /**
 * Sync all active project Notes directories into the Obsidian vault.
 *
-* For each active project that has at least one Notes source, creates:
-*
+* For each active project with at least one Notes source, creates:
 *   {vault}/{slug}/           — real directory
-*     notes    → {root}/Notes/                       (if project root Notes exists)
-*     sessions → ~/.claude/projects/{enc}/Notes/     (if Claude Code session notes exist)
+*     notes    → {root}/Notes/
+*     sessions → ~/.claude/projects/{enc}/Notes/  (if different)
 *
-* Projects with neither source are skipped.
 * Archived projects get a stub markdown file in {vault}/_archive/.
 */
 function syncVault(vaultPath, db) {
@@ -5558,6 +5592,10 @@ function syncVault(vaultPath, db) {
 	}
 	return stats;
 }
+
+//#endregion
+//#region src/obsidian/sync/generate.ts
+/** Index and topic page generation — writes _index.md and _topics/{tag}.md. */
 /**
 * Generate _index.md listing all projects with session counts, tags, and
 * indicators for which note sources are available (notes, sessions, or both).
@@ -5652,14 +5690,14 @@ function generateTopicPages(vaultPath, db) {
 function defaultVaultPath() {
 	return join(homedir(), ".pai", "obsidian-vault");
 }
+
+//#endregion
+//#region src/obsidian/sync/walk.ts
+/** Directory walking and session file discovery for vault note generation. */
 const SESSION_FILENAME_RE = /^(\d{4}) - (\d{4}-\d{2})-\d{2} - .+\.md$/;
-/** Build the per-project master note filename. */
-function masterFilename(slug) {
-	return `_${slug}-master.md`;
-}
 /**
-* Walk a directory (non-recursive, then one level of YYYY/MM subdirs).
-* Returns absolute paths to all .md files found.
+* Walk a directory (non-recursive root level, then one level of YYYY/MM subdirs).
+* Returns absolute paths to all .md files found, skipping master note files.
 */
 function walkNotesDir(dir) {
 	const results = [];
@@ -5707,7 +5745,7 @@ function walkNotesDir(dir) {
 }
 /**
 * Extract YYYY/MM from a session file path.
-* Tries the path first (looks for /YYYY/MM/ pattern), then falls back to filename date.
+* Tries the path first (/YYYY/MM/ pattern), then falls back to filename date.
 */
 function extractYearMonth(filePath) {
 	const pathMatch = filePath.match(/\/(\d{4})\/(\d{2})\//);
@@ -5717,8 +5755,50 @@ function extractYearMonth(filePath) {
 	return "unknown";
 }
 /**
+* Collect all session .md files from the notes and sessions symlinks
+* inside a vault project directory.
+*/
+function collectSessionFiles(slugPath) {
+	const sessionFiles = [];
+	for (const subLink of ["notes", "sessions"]) {
+		const linkPath = join(slugPath, subLink);
+		if (!existsSync(linkPath)) continue;
+		let realDir;
+		try {
+			const stat = lstatSync(linkPath);
+			if (stat.isSymbolicLink()) realDir = readlinkSync(linkPath);
+			else if (stat.isDirectory()) realDir = linkPath;
+			else continue;
+		} catch {
+			continue;
+		}
+		const files = walkNotesDir(realDir);
+		for (const absPath of files) {
+			const basename = absPath.split("/").pop() ?? "";
+			if (!SESSION_FILENAME_RE.test(basename)) continue;
+			const vaultRelPath = `${subLink}/${relative(realDir, absPath)}`;
+			const wikilinkTarget = vaultRelPath.replace(/\.md$/, "");
+			sessionFiles.push({
+				absPath,
+				vaultRelPath,
+				wikilinkTarget,
+				yearMonth: extractYearMonth(absPath),
+				basename: basename.replace(/\.md$/, "")
+			});
+		}
+	}
+	return sessionFiles;
+}
+
+//#endregion
+//#region src/obsidian/sync/master.ts
+/** Master note generation and session tag fixing for vault projects. */
+/** Build the per-project master note filename. */
+function masterFilename(slug) {
+	return `_${slug}-master.md`;
+}
+/**
 * Remove any old/broken backlink footer from a session file.
-* Matches the old [[../_master|...]] pattern as well as any [[_{slug}-master|...]] footer.
 * Returns true if the file was modified.
 */
 function removeOldBacklink(filePath) {
@@ -5739,8 +5819,7 @@ function removeOldBacklink(filePath) {
 }
 /**
 * Append the master note backlink footer to a session file, idempotently.
-* Uses Obsidian filename-based wikilink (resolves from anywhere in the vault).
-* Only writes if the sentinel string is not already present in the file.
+* Only writes if the sentinel string is not already present.
 */
 function appendBacklinkIfMissing(filePath, slug, displayName) {
 	let content;
@@ -5761,12 +5840,10 @@ function appendBacklinkIfMissing(filePath, slug, displayName) {
 	}
 }
 /**
-* Generate _master.md files for projects that have enough sessions.
+* Generate _master.md files for projects that have >= threshold session files.
 *
-* For each project directory in the vault that has >= threshold session files,
-* writes a {vaultPath}/{slug}/_master.md containing:
-*   - Project title
-*   - Session count + date range
+* For each qualifying project, writes a {vaultPath}/{slug}/_master.md containing:
+*   - Project title, session count + date range
 *   - Sessions grouped by YYYY/MM with Obsidian [[wikilinks]]
 *
 * Also appends a backlink footer to each session file (idempotently).
@@ -5790,34 +5867,7 @@ function generateMasterNotes(vaultPath, db, threshold = 5) {
 		if (existsSync(legacyMaster)) try {
 			unlinkSync(legacyMaster);
 		} catch {}
-		const sessionFiles = [];
-		for (const subLink of ["notes", "sessions"]) {
-			const linkPath = join(slugPath, subLink);
-			if (!existsSync(linkPath)) continue;
-			let realDir;
-			try {
-				const stat = lstatSync(linkPath);
-				if (stat.isSymbolicLink()) realDir = readlinkSync(linkPath);
-				else if (stat.isDirectory()) realDir = linkPath;
-				else continue;
-			} catch {
-				continue;
-			}
-			const files = walkNotesDir(realDir);
-			for (const absPath of files) {
-				const basename = absPath.split("/").pop() ?? "";
-				if (!SESSION_FILENAME_RE.test(basename)) continue;
-				const vaultRelPath = `${subLink}/${relative(realDir, absPath)}`;
-				const wikilinkTarget = vaultRelPath.replace(/\.md$/, "");
-				sessionFiles.push({
-					absPath,
-					vaultRelPath,
-					wikilinkTarget,
-					yearMonth: extractYearMonth(absPath),
-					basename: basename.replace(/\.md$/, "")
-				});
-			}
-		}
+		const sessionFiles = collectSessionFiles(slugPath);
 		if (sessionFiles.length < threshold) continue;
 		sessionFiles.sort((a, b) => {
 			if (a.yearMonth !== b.yearMonth) return a.yearMonth.localeCompare(b.yearMonth);
@@ -5867,12 +5917,8 @@ function generateMasterNotes(vaultPath, db, threshold = 5) {
 /**
 * Remove the generic #Session tag from session note files across all projects.
 *
-* Session notes are written with `**Tags:** #Session ...` but the generic #Session
-* tag is not useful — each note already belongs to a project. This function scans
-* all session and notes directories for every active project and removes #Session
-* (with or without a trailing space) from any `**Tags:**` line.
-*
-* The project-specific tags that follow #Session are preserved untouched.
+* Scans all session and notes directories for every active project and removes
+* #Session (with or without a trailing space) from any `**Tags:**` line.
 *
 * @param db  Registry SQLite database
 * @returns   Object with counts: { filesScanned, filesModified, errors }
@@ -5889,7 +5935,9 @@ function fixSessionTags(db) {
        ORDER BY slug ASC`).all();
 	for (const project of projects) {
 		const dirsToScan = [];
-		const notesDir = findNotesDir(project.root_path);
+		const canonical = join(project.root_path, "Notes");
+		const alt = join(project.root_path, ".claude", "Notes");
+		const notesDir = existsSync(canonical) ? canonical : existsSync(alt) ? alt : null;
 		if (notesDir) dirsToScan.push(notesDir);
 		if (project.claude_notes_dir && existsSync(project.claude_notes_dir) && project.claude_notes_dir !== notesDir) dirsToScan.push(project.claude_notes_dir);
 		for (const dir of dirsToScan) {
@@ -6225,8 +6273,13 @@ function registerObsidianCommands(obsidianCmd, getDb) {
 }
 
 //#endregion
-//#region src/cli/commands/zettel.ts
+//#region src/cli/commands/zettel/utils.ts
+/** Shorten a vault path to just the last 2-3 components for display. */
+function shortPath(p, parts = 3) {
+	return p.split("/").filter(Boolean).slice(-parts).join("/");
+}
 let _fedDb = null;
+/** Get (or lazily open) the PAI federation database. */
 function getFedDb() {
 	if (!_fedDb) try {
 		_fedDb = openFederation();
@@ -6236,15 +6289,14 @@ function getFedDb() {
 	}
 	return _fedDb;
 }
-/** Shorten a vault path to just the last 2-3 components for display. */
-function shortPath(p, parts = 3) {
-	return p.split("/").filter(Boolean).slice(-parts).join("/");
-}
+
+//#endregion
+//#region src/cli/commands/zettel/explore.ts
 async function cmdExplore(note, opts) {
 	const depth = parseInt(opts.depth ?? "3", 10);
 	const direction = opts.direction ?? "both";
 	const mode = opts.mode ?? "all";
-	const { zettelExplore } = await import("../zettelkasten-e-a4rW_6.mjs");
+	const { zettelExplore } = await import("../zettelkasten-cdajbnPr.mjs");
 	const result = zettelExplore(getFedDb(), {
 		startNote: note,
 		depth,
@@ -6290,12 +6342,25 @@ async function cmdExplore(note, opts) {
 	if (result.maxDepthReached) console.log(warn("  Max depth reached — use --depth to explore further"));
 	console.log();
 }
+function registerExploreCommand(parent) {
+	parent.command("explore <note>").description("Follow link chains from a starting note").option("--depth <n>", "Maximum traversal depth (1-10)", "3").option("--direction <d>", "Link direction: forward | backward | both", "both").option("--mode <m>", "Edge mode: sequential | associative | all", "all").action(async (note, opts) => {
+		try {
+			await cmdExplore(note, opts);
+		} catch (e) {
+			console.error(err(`  Error: ${e}`));
+			process.exit(1);
+		}
+	});
+}
+
+//#endregion
+//#region src/cli/commands/zettel/health.ts
 async function cmdHealth(opts) {
 	const scope = opts.scope ?? "full";
 	const projectPath = opts.project;
 	const recentDays = parseInt(opts.days ?? "30", 10);
 	const includeTypes = opts.include ? opts.include.split(",").map((s) => s.trim()) : void 0;
-	const { zettelHealth } = await import("../zettelkasten-e-a4rW_6.mjs");
+	const { zettelHealth } = await import("../zettelkasten-cdajbnPr.mjs");
 	const result = zettelHealth(getFedDb(), {
 		scope,
 		projectPath,
@@ -6342,6 +6407,19 @@ async function cmdHealth(opts) {
 	}
 	console.log();
 }
+function registerHealthCommand(parent) {
+	parent.command("health").description("Vault structural health audit: dead links, orphans, connectivity").option("--scope <s>", "Scope: full | recent | project", "full").option("--project <path>", "Project path prefix (requires --scope project)").option("--days <n>", "Look-back window in days (requires --scope recent)", "30").option("--include <types>", "Comma-separated subset: dead_links,orphans,disconnected,low_connectivity").action(async (opts) => {
+		try {
+			await cmdHealth(opts);
+		} catch (e) {
+			console.error(err(`  Error: ${e}`));
+			process.exit(1);
+		}
+	});
+}
+
+//#endregion
+//#region src/cli/commands/zettel/surprise.ts
 async function cmdSurprise(note, opts) {
 	if (!opts.vaultProjectId) {
 		console.error(err("  --vault-project-id is required"));
@@ -6351,7 +6429,7 @@ async function cmdSurprise(note, opts) {
 	const limit = parseInt(opts.limit ?? "10", 10);
 	const minSimilarity = parseFloat(opts.minSimilarity ?? "0.3");
 	const minGraphDistance = parseInt(opts.minDistance ?? "3", 10);
-	const { zettelSurprise } = await import("../zettelkasten-e-a4rW_6.mjs");
+	const { zettelSurprise } = await import("../zettelkasten-cdajbnPr.mjs");
 	const db = getFedDb();
 	console.log();
 	console.log(header("  PAI Zettel Surprise"));
@@ -6383,6 +6461,19 @@ async function cmdSurprise(note, opts) {
 		console.log();
 	}
 }
+function registerSurpriseCommand(parent) {
+	parent.command("surprise <note>").description("Find semantically similar but graph-distant notes (surprising connections)").requiredOption("--vault-project-id <n>", "Project ID for the vault in the federation DB").option("--limit <n>", "Maximum results", "10").option("--min-similarity <f>", "Minimum cosine similarity (0–1)", "0.3").option("--min-distance <n>", "Minimum graph distance", "3").action(async (note, opts) => {
+		try {
+			await cmdSurprise(note, opts);
+		} catch (e) {
+			console.error(err(`  Error: ${e}`));
+			process.exit(1);
+		}
+	});
+}
+
+//#endregion
+//#region src/cli/commands/zettel/suggest.ts
 async function cmdSuggest(note, opts) {
 	if (!opts.vaultProjectId) {
 		console.error(err("  --vault-project-id is required"));
@@ -6391,7 +6482,7 @@ async function cmdSuggest(note, opts) {
 	const vaultProjectId = parseInt(opts.vaultProjectId, 10);
 	const limit = parseInt(opts.limit ?? "5", 10);
 	const excludeLinked = opts.excludeLinked !== false;
-	const { zettelSuggest } = await import("../zettelkasten-e-a4rW_6.mjs");
+	const { zettelSuggest } = await import("../zettelkasten-cdajbnPr.mjs");
 	const db = getFedDb();
 	console.log();
 	console.log(header("  PAI Zettel Suggest"));
@@ -6421,6 +6512,19 @@ async function cmdSuggest(note, opts) {
 		console.log();
 	}
 }
+function registerSuggestCommand(parent) {
+	parent.command("suggest <note>").description("Suggest new wikilink connections for a note").requiredOption("--vault-project-id <n>", "Project ID for the vault in the federation DB").option("--limit <n>", "Maximum suggestions", "5").option("--no-exclude-linked", "Include notes already linked from this one").action(async (note, opts) => {
+		try {
+			await cmdSuggest(note, opts);
+		} catch (e) {
+			console.error(err(`  Error: ${e}`));
+			process.exit(1);
+		}
+	});
+}
+
+//#endregion
+//#region src/cli/commands/zettel/converse.ts
 async function cmdConverse(question, opts) {
 	if (!opts.vaultProjectId) {
 		console.error(err("  --vault-project-id is required"));
@@ -6429,7 +6533,7 @@ async function cmdConverse(question, opts) {
 	const vaultProjectId = parseInt(opts.vaultProjectId, 10);
 	const depth = parseInt(opts.depth ?? "2", 10);
 	const limit = parseInt(opts.limit ?? "15", 10);
-	const { zettelConverse } = await import("../zettelkasten-e-a4rW_6.mjs");
+	const { zettelConverse } = await import("../zettelkasten-cdajbnPr.mjs");
 	const db = getFedDb();
 	console.log();
 	console.log(header("  PAI Zettel Converse"));
@@ -6467,6 +6571,19 @@ async function cmdConverse(question, opts) {
 	for (const line of promptLines) console.log(`  ${dim(line)}`);
 	console.log();
 }
+function registerConverseCommand(parent) {
+	parent.command("converse <question>").description("Ask the vault a question and get a synthesis prompt with relevant notes").requiredOption("--vault-project-id <n>", "Project ID for the vault in the federation DB").option("--depth <n>", "Graph expansion depth around matched notes", "2").option("--limit <n>", "Maximum relevant notes to include", "15").action(async (question, opts) => {
+		try {
+			await cmdConverse(question, opts);
+		} catch (e) {
+			console.error(err(`  Error: ${e}`));
+			process.exit(1);
+		}
+	});
+}
+
+//#endregion
+//#region src/cli/commands/zettel/themes.ts
 async function cmdThemes(opts) {
 	if (!opts.vaultProjectId) {
 		console.error(err("  --vault-project-id is required"));
@@ -6477,7 +6594,7 @@ async function cmdThemes(opts) {
 	const minClusterSize = parseInt(opts.minSize ?? "3", 10);
 	const maxThemes = parseInt(opts.maxThemes ?? "10", 10);
 	const similarityThreshold = parseFloat(opts.threshold ?? "0.65");
-	const { zettelThemes } = await import("../zettelkasten-e-a4rW_6.mjs");
+	const { zettelThemes } = await import("../zettelkasten-cdajbnPr.mjs");
 	const db = getFedDb();
 	console.log();
 	console.log(header("  PAI Zettel Themes"));
@@ -6515,50 +6632,260 @@ async function cmdThemes(opts) {
 		console.log();
 	}
 }
-function registerZettelCommands(parent, _getDb) {
-	parent.command("explore <note>").description("Follow link chains from a starting note").option("--depth <n>", "Maximum traversal depth (1-10)", "3").option("--direction <d>", "Link direction: forward | backward | both", "both").option("--mode <m>", "Edge mode: sequential | associative | all", "all").action(async (note, opts) => {
+function registerThemesCommand(parent) {
+	parent.command("themes").description("Detect emerging theme clusters in recently edited notes").requiredOption("--vault-project-id <n>", "Project ID for the vault in the federation DB").option("--days <n>", "Look-back window in days", "30").option("--min-size <n>", "Minimum notes per cluster", "3").option("--max-themes <n>", "Maximum themes to return", "10").option("--threshold <f>", "Similarity threshold for clustering (0–1)", "0.65").action(async (opts) => {
 		try {
-			await cmdExplore(note, opts);
+			await cmdThemes(opts);
 		} catch (e) {
 			console.error(err(`  Error: ${e}`));
 			process.exit(1);
 		}
 	});
-	parent.command("health").description("Vault structural health audit: dead links, orphans, connectivity").option("--scope <s>", "Scope: full | recent | project", "full").option("--project <path>", "Project path prefix (requires --scope project)").option("--days <n>", "Look-back window in days (requires --scope recent)", "30").option("--include <types>", "Comma-separated subset: dead_links,orphans,disconnected,low_connectivity").action(async (opts) => {
-		try {
-			await cmdHealth(opts);
-		} catch (e) {
-			console.error(err(`  Error: ${e}`));
-			process.exit(1);
-		}
+}
+
+//#endregion
+//#region src/cli/commands/zettel/index.ts
+function registerZettelCommands(parent, _getDb) {
+	registerExploreCommand(parent);
+	registerHealthCommand(parent);
+	registerSurpriseCommand(parent);
+	registerSuggestCommand(parent);
+	registerConverseCommand(parent);
+	registerThemesCommand(parent);
+}
+
+//#endregion
+//#region src/cli/commands/observation.ts
+function ipcCall(method, params) {
+	return new Promise((resolve, reject) => {
+		let settled = false;
+		const settle = (fn) => {
+			if (!settled) {
+				settled = true;
+				fn();
+			}
+		};
+		const client = createConnection("/tmp/pai.sock", () => {
+			client.write(JSON.stringify({
+				id: 1,
+				method,
+				params
+			}) + "\n");
+		});
+		let data = "";
+		client.on("data", (chunk) => {
+			data += chunk.toString();
+			try {
+				const resp = JSON.parse(data);
+				client.end();
+				settle(() => resp.ok ? resolve(resp.result) : reject(new Error(resp.error ?? "IPC call failed")));
+			} catch {}
+		});
+		client.on("end", () => {
+			settle(() => {
+				try {
+					const resp = JSON.parse(data);
+					resp.ok ? resolve(resp.result) : reject(new Error(resp.error ?? "IPC call failed"));
+				} catch (e) {
+					reject(e);
+				}
+			});
+		});
+		client.on("error", (e) => settle(() => reject(e)));
+		setTimeout(() => {
+			client.destroy();
+			settle(() => reject(/* @__PURE__ */ new Error("IPC timeout")));
+		}, 1e4);
 	});
-	parent.command("surprise <note>").description("Find semantically similar but graph-distant notes (surprising connections)").requiredOption("--vault-project-id <n>", "Project ID for the vault in the federation DB").option("--limit <n>", "Maximum results", "10").option("--min-similarity <f>", "Minimum cosine similarity (0–1)", "0.3").option("--min-distance <n>", "Minimum graph distance", "3").action(async (note, opts) => {
-		try {
-			await cmdSurprise(note, opts);
-		} catch (e) {
-			console.error(err(`  Error: ${e}`));
-			process.exit(1);
+}
+function typeColor(type) {
+	switch (type) {
+		case "decision": return chalk.cyan(type);
+		case "bugfix": return chalk.red(type);
+		case "feature": return chalk.green(type);
+		case "refactor": return chalk.yellow(type);
+		case "discovery": return chalk.blue(type);
+		case "change": return chalk.magenta(type);
+		default: return chalk.white(type);
+	}
+}
+function fmtTs(ts) {
+	if (!ts) return dim("—");
+	try {
+		const d = new Date(ts);
+		return `${d.toISOString().slice(0, 10)} ${d.toISOString().slice(11, 16)}`;
+	} catch {
+		return dim("—");
+	}
+}
+function trunc(s, maxLen) {
+	if (!s) return "";
+	if (s.length <= maxLen) return s;
+	return s.slice(0, maxLen - 1) + "…";
+}
+async function cmdList(opts) {
+	const limit = parseInt(opts.limit ?? "20", 10);
+	const params = { limit };
+	if (opts.project) params.project_slug = opts.project;
+	if (opts.type) params.type = opts.type;
+	if (opts.session) params.session_id = opts.session;
+	let observations;
+	try {
+		observations = await ipcCall("observation_list", params);
+	} catch (e) {
+		console.error(err(`  Failed to reach PAI daemon: ${e}`));
+		console.error(dim("  Is the daemon running? Try: pai daemon status"));
+		process.exit(1);
+	}
+	console.log();
+	console.log(header("  PAI Observations"));
+	const filterParts = [];
+	if (opts.project) filterParts.push(`project: ${opts.project}`);
+	if (opts.type) filterParts.push(`type: ${opts.type}`);
+	if (opts.session) filterParts.push(`session: ${opts.session}`);
+	filterParts.push(`limit: ${limit}`);
+	console.log(dim(`  ${filterParts.join("  |  ")}`));
+	console.log();
+	if (!observations || observations.length === 0) {
+		console.log(warn("  No observations found."));
+		console.log();
+		return;
+	}
+	const ID_W = 4;
+	const TYPE_W = 10;
+	const TITLE_W = 42;
+	const PROJ_W = 14;
+	const TS_W = 16;
+	console.log("  " + bold("id".padEnd(ID_W)) + "  " + bold("type".padEnd(TYPE_W)) + "  " + bold("title".padEnd(TITLE_W)) + "  " + bold("project".padEnd(PROJ_W)) + "  " + bold("created_at"));
+	console.log(dim("  " + "-".repeat(ID_W) + "  " + "-".repeat(TYPE_W) + "  " + "-".repeat(TITLE_W) + "  " + "-".repeat(PROJ_W) + "  " + "-".repeat(TS_W)));
+	for (const obs of observations) {
+		const idStr = String(obs.id).padStart(ID_W, " ");
+		const typeStr = typeColor(obs.type ?? "").padEnd(TYPE_W + (typeColor(obs.type ?? "").length - (obs.type ?? "").length));
+		const titleStr = trunc(obs.title ?? "", TITLE_W).padEnd(TITLE_W);
+		const projStr = trunc(obs.project_slug ?? "—", PROJ_W).padEnd(PROJ_W);
+		const tsStr = fmtTs(obs.created_at);
+		console.log(`  ${idStr}  ${typeStr}  ${titleStr}  ${projStr}  ${dim(tsStr)}`);
+	}
+	console.log();
+	console.log(dim(`  ${observations.length} observation(s)`));
+	console.log();
+}
+async function cmdSearch(query, opts) {
+	const limit = parseInt(opts.limit ?? "20", 10);
+	const params = {
+		query,
+		limit
+	};
+	if (opts.project) params.project_slug = opts.project;
+	if (opts.type) params.type = opts.type;
+	let allObservations;
+	try {
+		allObservations = await ipcCall("observation_query", {
+			...params,
+			limit: limit * 5,
+			query: void 0
+		});
+	} catch (e) {
+		console.error(err(`  Failed to reach PAI daemon: ${e}`));
+		console.error(dim("  Is the daemon running? Try: pai daemon status"));
+		process.exit(1);
+	}
+	const q = query.toLowerCase();
+	const observations = allObservations.filter((o) => (o.title ?? "").toLowerCase().includes(q) || (o.narrative ?? "").toLowerCase().includes(q) || (o.tool_input_summary ?? "").toLowerCase().includes(q)).slice(0, limit);
+	console.log();
+	console.log(header("  PAI Observation Search"));
+	console.log(dim(`  Query: "${query}"${opts.project ? `  project: ${opts.project}` : ""}${opts.type ? `  type: ${opts.type}` : ""}  limit: ${limit}`));
+	console.log();
+	if (!observations || observations.length === 0) {
+		console.log(warn(`  No observations matching "${query}".`));
+		console.log();
+		return;
+	}
+	for (let i = 0; i < observations.length; i++) {
+		const obs = observations[i];
+		const idx = chalk.dim(String(i + 1).padStart(3, " "));
+		const type = typeColor(obs.type ?? "");
+		const title = bold(obs.title ?? "(untitled)");
+		const proj = obs.project_slug ? dim(`[${obs.project_slug}]`) : dim("[—]");
+		const ts = dim(fmtTs(obs.created_at));
+		const id = dim(`#${obs.id}`);
+		console.log(`  ${idx}  ${type.padEnd(12)}  ${title}`);
+		console.log(`           ${proj}  ${ts}  ${id}`);
+		if (obs.narrative) {
+			const snippet = trunc(obs.narrative.replace(/\n/g, " "), 160);
+			console.log(`           ${dim(snippet)}`);
 		}
-	});
-	parent.command("suggest <note>").description("Suggest new wikilink connections for a note").requiredOption("--vault-project-id <n>", "Project ID for the vault in the federation DB").option("--limit <n>", "Maximum suggestions", "5").option("--no-exclude-linked", "Include notes already linked from this one").action(async (note, opts) => {
+		console.log();
+	}
+	console.log(dim(`  ${observations.length} result(s)`));
+	console.log();
+}
+async function cmdStats() {
+	let stats;
+	try {
+		stats = await ipcCall("observation_stats", {});
+	} catch (e) {
+		console.error(err(`  Failed to reach PAI daemon: ${e}`));
+		console.error(dim("  Is the daemon running? Try: pai daemon status"));
+		process.exit(1);
+	}
+	console.log();
+	console.log(header("  PAI Observation Statistics"));
+	console.log();
+	console.log(`  ${bold("Total observations:")}  ${chalk.cyan(String(stats.total ?? 0))}`);
+	if (stats.most_recent) console.log(`  ${bold("Most recent:")}         ${dim(fmtTs(stats.most_recent))}`);
+	console.log();
+	if (stats.by_type && stats.by_type.length > 0) {
+		console.log(bold("  By type:"));
+		const maxCount = Math.max(...stats.by_type.map((r) => r.count));
+		for (const row of stats.by_type) {
+			const barWidth = 20;
+			const filled = Math.round(row.count / maxCount * barWidth);
+			const bar = chalk.cyan("█".repeat(filled)) + dim("░".repeat(barWidth - filled));
+			const label = typeColor(row.type).padEnd(12 + (typeColor(row.type).length - row.type.length));
+			console.log(`    ${label}  ${bar}  ${String(row.count).padStart(5)}`);
+		}
+		console.log();
+	}
+	if (stats.by_project && stats.by_project.length > 0) {
+		console.log(bold("  By project:"));
+		const maxCount = Math.max(...stats.by_project.map((r) => r.count));
+		const show = stats.by_project.slice(0, 15);
+		for (const row of show) {
+			const barWidth = 20;
+			const filled = Math.round(row.count / maxCount * barWidth);
+			const bar = chalk.green("█".repeat(filled)) + dim("░".repeat(barWidth - filled));
+			const label = (row.project_slug ?? "—").padEnd(20);
+			console.log(`    ${dim(label)}  ${bar}  ${String(row.count).padStart(5)}`);
+		}
+		if (stats.by_project.length > 15) console.log(dim(`    ... and ${stats.by_project.length - 15} more project(s)`));
+		console.log();
+	}
+	if ((!stats.by_type || stats.by_type.length === 0) && (!stats.by_project || stats.by_project.length === 0)) {
+		console.log(warn("  No observation data yet."));
+		console.log();
+	}
+}
+function registerObservationCommands(parent) {
+	parent.command("list").description("List recent observations").option("--project <slug>", "Filter by project slug").option("--type <type>", "Filter by type (decision, bugfix, feature, refactor, discovery, change)").option("--session <id>", "Filter by session ID").option("--limit <n>", "Maximum results", "20").action(async (opts) => {
 		try {
-			await cmdSuggest(note, opts);
+			await cmdList(opts);
 		} catch (e) {
 			console.error(err(`  Error: ${e}`));
 			process.exit(1);
 		}
 	});
-	parent.command("converse <question>").description("Ask the vault a question and get a synthesis prompt with relevant notes").requiredOption("--vault-project-id <n>", "Project ID for the vault in the federation DB").option("--depth <n>", "Graph expansion depth around matched notes", "2").option("--limit <n>", "Maximum relevant notes to include", "15").action(async (question, opts) => {
+	parent.command("search <query>").description("Search observations by title or narrative text").option("--project <slug>", "Filter by project slug").option("--type <type>", "Filter by type").option("--limit <n>", "Maximum results", "20").action(async (query, opts) => {
 		try {
-			await cmdConverse(question, opts);
+			await cmdSearch(query, opts);
 		} catch (e) {
 			console.error(err(`  Error: ${e}`));
 			process.exit(1);
 		}
 	});
-	parent.command("themes").description("Detect emerging theme clusters in recently edited notes").requiredOption("--vault-project-id <n>", "Project ID for the vault in the federation DB").option("--days <n>", "Look-back window in days", "30").option("--min-size <n>", "Minimum notes per cluster", "3").option("--max-themes <n>", "Maximum themes to return", "10").option("--threshold <f>", "Similarity threshold for clustering (0–1)", "0.65").action(async (opts) => {
+	parent.command("stats").description("Show observation statistics: totals, by type, by project").action(async () => {
 		try {
-			await cmdThemes(opts);
+			await cmdStats();
 		} catch (e) {
 			console.error(err(`  Error: ${e}`));
 			process.exit(1);
@@ -6870,7 +7197,7 @@ function registerUpdateCommand(program) {
 //#endregion
 //#region src/cli/commands/notify.ts
 function makeClient$1() {
-	return new PaiClient(loadConfig$1().socketPath);
+	return new PaiClient(loadConfig().socketPath);
 }
 function modeColor(mode) {
 	switch (mode) {
@@ -7052,7 +7379,7 @@ function registerNotifyCommands(notifyCmd) {
 //#endregion
 //#region src/cli/commands/topic.ts
 function makeClient() {
-	return new PaiClient(loadConfig$1().socketPath);
+	return new PaiClient(loadConfig().socketPath);
 }
 function confidenceBar(confidence, width = 20) {
 	const filled = Math.round(confidence * width);
@@ -7177,6 +7504,7 @@ registerNotifyCommands(program.command("notify").description("Notification confi
 registerTopicCommands(program.command("topic").description("Topic shift detection: check whether context has drifted to a different project"));
 registerObsidianCommands(program.command("obsidian").description("Obsidian vault: sync project notes, view status, open in Obsidian"), getDb);
 registerZettelCommands(program.command("zettel").description("Zettelkasten intelligence: explore, surprise, converse, themes, health, suggest"), getDb);
+registerObservationCommands(program.command("observation").description("Observation capture: list, search, and stats"));
 program.command("go <query>").description("Jump to a project directory by slug or partial name.\nPrints the root path to stdout — use with: cd $(pai go <query>)\nExample shell function in ~/.zshrc:\n  pcd() { cd \"$(pai go \"$@\")\" }").action((query) => {
 	cmdGo(getDb(), query);
 });