dotmd-cli 0.7.6 → 0.8.0

package/README.md

@@ -34,16 +34,19 @@ eval "$(dotmd completions zsh)"     # add to ~/.zshrc
 
 ## What It Does
 
-dotmd scans a directory of markdown files, parses their YAML frontmatter, and gives you tools to work with them:
-
 - **Index** — group docs by status, show progress bars, next steps
 - **Query** — filter by status, keyword, module, surface, owner, staleness
-- **Validate** — check for missing fields, broken references, stale dates, broken body links
+- **Validate** — check for missing fields, broken references, broken body links, stale dates
+- **Stats** — health dashboard with staleness, completeness, audit coverage
 - **Graph** — visualize document relationships as text, Graphviz DOT, or JSON
+- **Deps** — dependency tree or overview of what blocks what
 - **Lifecycle** — transition statuses, auto-archive with `git mv` and reference updates
 - **Doctor** — auto-fix broken refs, lint issues, date drift, and stale indexes in one pass
 - **Scaffold** — create new docs from templates (plan, ADR, RFC, audit, design)
-- **Index generation** — auto-generate a `docs.md` index block
+- **AI summaries** — summarize docs via local MLX model or custom hook
+- **Export** — generate concatenated markdown, static HTML site, or JSON bundle
+- **Notion** — import from, export to, and bidirectionally sync with Notion databases
+- **Multi-root** — manage docs across multiple directories with a single config
 - **Context briefing** — compact summary designed for AI/LLM consumption
 - **Dry-run** — preview any mutation with `--dry-run` before committing
 
@@ -72,17 +75,19 @@ Design doc content here...
 - [ ] Add tests
 ```
 
-The only required field is `status`. Everything else is optional but unlocks more features (staleness detection, filtering, coverage reports, graph visualization).
+The only required field is `status`. Everything else is optional but unlocks more features.
 
 ## Commands
 
 ```
 dotmd list [--verbose]       List docs grouped by status (default)
 dotmd json                   Full index as JSON
-dotmd check [--errors-only] [--fix]  Validate frontmatter and references
+dotmd check [flags]          Validate frontmatter and references
 dotmd coverage [--json]      Metadata coverage report
+dotmd stats [--json]         Doc health dashboard
 dotmd graph [--dot|--json]   Visualize document relationships
-dotmd context                Compact briefing (LLM-oriented)
+dotmd deps [file]            Dependency tree or overview
+dotmd context [--summarize]  Compact briefing (LLM-oriented)
 dotmd focus [status]         Detailed view for one status group
 dotmd query [filters]        Filtered search
 dotmd index [--write]        Generate/update docs.md index block
@@ -95,6 +100,9 @@ dotmd fix-refs               Auto-fix broken reference paths
 dotmd lint [--fix]           Check and auto-fix frontmatter issues
 dotmd rename <old> <new>     Rename doc and update references
 dotmd migrate <f> <old> <new>  Batch update a frontmatter field
+dotmd notion <sub> [db-id]   Notion import/export/sync
+dotmd export [file]          Export docs as md, html, or json
+dotmd summary <file>         AI summary of a document
 dotmd watch [command]        Re-run a command on file changes
 dotmd diff [file]            Show changes since last updated date
 dotmd new <name>             Create a new document from template
@@ -107,6 +115,7 @@ dotmd completions <shell>    Output shell completion script (bash, zsh)
 ```
 --config <path>        Explicit config file path
 --dry-run, -n          Preview changes without writing anything
+--root <name>          Filter to a specific docs root
 --verbose              Show resolved config details
 --help, -h             Show help (per-command with: dotmd <cmd> --help)
 --version, -v          Show version
@@ -119,9 +128,11 @@ dotmd query --status active,ready --module auth
 dotmd query --keyword "token" --has-next-step
 dotmd query --stale --sort updated --all
 dotmd query --surface backend --checklist-open
+dotmd query --status active --summarize             # AI summaries
+dotmd query --status active --summarize --summarize-limit 3
 ```
 
-Flags: `--status`, `--keyword`, `--module`, `--surface`, `--domain`, `--owner`, `--updated-since`, `--stale`, `--has-next-step`, `--has-blockers`, `--checklist-open`, `--sort`, `--limit`, `--all`, `--git`, `--json`.
+Flags: `--status`, `--keyword`, `--module`, `--surface`, `--domain`, `--owner`, `--updated-since`, `--stale`, `--has-next-step`, `--has-blockers`, `--checklist-open`, `--sort`, `--limit`, `--all`, `--git`, `--json`, `--summarize`, `--summarize-limit`, `--model`.
 
 ### Scaffold with Templates
 
@@ -133,6 +144,7 @@ dotmd new my-proposal --template rfc                  # RFC: Summary, Motivation
 dotmd new my-audit --template audit                   # Audit: Scope, Findings, Recommendations
 dotmd new my-design --template design                 # Design: Goals, Non-Goals, Design
 dotmd new my-feature --status planned --title "Title" # custom status and title
+dotmd new my-doc --root modules                       # create in a specific root
 dotmd new --list-templates                            # show all available templates
 ```
 
@@ -158,21 +170,24 @@ dotmd check --fix            # auto-fix broken refs + lint + regen index
 
 Validates: required fields, status values, broken reference paths, broken body links (`[text](path.md)`), bidirectional reference symmetry, git date drift, taxonomy mismatches.
 
-### Doctor
+### Stats
 
-One command to fix everything fixable:
+```bash
+dotmd stats                  # health dashboard
+dotmd stats --json           # machine-readable
+```
+
+Shows: status counts, staleness, errors/warnings, freshness (today/week/month), completeness (owner/surface/module/next_step), checklist progress, audit coverage.
+
+### Doctor
 
 ```bash
 dotmd doctor                 # fix refs → lint → sync git dates → regen index
 dotmd doctor --dry-run       # preview all changes
 ```
 
-Runs in sequence: `fix-refs` → `lint --fix` → `touch --git` → `index --write` → shows remaining issues.
-
 ### Graph
 
-Visualize how documents reference each other:
-
 ```bash
 dotmd graph                              # text adjacency list
 dotmd graph --dot | dot -Tpng -o g.png   # Graphviz PNG
@@ -181,6 +196,78 @@ dotmd graph --status active,ready        # filter by status
 dotmd graph --module auth                # filter by module
 ```
 
+### Deps
+
+```bash
+dotmd deps                               # overview: most blocking, most blocked
+dotmd deps docs/plan-a.md                # tree: depends-on + depended-on-by
+dotmd deps docs/plan-a.md --depth 2      # limit tree depth
+dotmd deps --json                        # machine-readable
+```
+
+### AI Summaries
+
+```bash
+dotmd summary docs/plan-a.md             # AI summary of a single doc
+dotmd summary docs/plan-a.md --json      # JSON output
+dotmd query --status active --summarize  # AI summaries in query results
+dotmd context --summarize                # AI-enhanced briefing
+```
+
+Uses local MLX model via `uv`. Override with `--model <name>` or the `summarizeDoc` hook.
+
+### Export
+
+```bash
+dotmd export                             # all docs as concatenated markdown
+dotmd export --format html --output site # static HTML site
+dotmd export --format json > bundle.json # JSON bundle with bodies
+dotmd export docs/plan-a.md              # single doc + dependencies
+dotmd export --status active             # filtered export
+```
+
+### Notion Integration
+
+```bash
+dotmd notion import <database-id>        # pull Notion database → local .md files
+dotmd notion export <database-id>        # push local docs → Notion database
+dotmd notion sync <database-id>          # bidirectional sync (newer wins)
+dotmd notion import <db-id> --force      # overwrite existing files
+dotmd notion sync <db-id> --dry-run      # preview sync actions
+```
+
+Requires `NOTION_TOKEN` env var or `notion.token` in config. Maps Notion properties (select, multi_select, date, status, people, etc.) to YAML frontmatter fields. Configure property mapping in config:
+
+```js
+export const notion = {
+  token: process.env.NOTION_TOKEN,
+  database: 'your-database-id',
+  propertyMap: {
+    'Status': 'status',
+    'Last Updated': 'updated',
+    'Tags': 'surfaces',
+  },
+};
+```
+
+### Multi-Root
+
+Manage docs across multiple directories:
+
+```js
+export const root = ['docs/plans', 'docs/modules', 'docs/app'];
+```
+
+All commands work across all roots. Filter with `--root`:
+
+```bash
+dotmd list --root plans                  # only docs from docs/plans
+dotmd stats --root modules               # stats for modules only
+dotmd new my-doc --root modules          # create in docs/modules
+```
+
+Archive stays within the source file's root. Cross-root references validate correctly.
+
 ### Archive
 
 ```bash
@@ -188,44 +275,33 @@ dotmd archive docs/old-plan.md           # move + update refs + regen index
 dotmd archive docs/old-plan.md -n        # preview
 ```
 
-Archives a document: sets status to `archived`, moves to archive directory via `git mv`, auto-updates references in other docs, and regenerates the index.
-
 ### Touch
 
 ```bash
 dotmd touch docs/my-doc.md              # set updated to today
 dotmd touch --git                        # bulk-sync all docs from git history
-dotmd touch --git docs/my-doc.md         # sync one file from git
 ```
 
 ### Fix References
 
 ```bash
-dotmd fix-refs                           # find and fix broken ref paths
+dotmd fix-refs                           # fix broken frontmatter refs + body links
 dotmd fix-refs --dry-run                 # preview fixes
 ```
 
-Scans all reference fields for broken paths, resolves by basename matching, and rewrites frontmatter.
-
 ### Lint
 
 ```bash
 dotmd lint                   # report issues
 dotmd lint --fix             # fix all issues
-dotmd lint --fix --dry-run   # preview fixes without writing
 ```
 
-Detected issues: missing `updated`, status casing, camelCase keys, trailing whitespace, missing EOF newline.
-
 ### Rename
 
 ```bash
 dotmd rename old-name.md new-name        # renames + updates refs
-dotmd rename old-name.md new-name -n     # preview without writing
 ```
 
-Uses `git mv` and updates all frontmatter references. Body markdown links are warned about but not auto-fixed.
-
 ### Migrate
 
 ```bash
@@ -261,12 +337,16 @@ dotmd diff --stat                    # summary stats only
 dotmd diff --summarize               # AI summary via local MLX model
 ```
 
+### Init Auto-Detect
+
+When `dotmd init` runs in a directory with existing `.md` files, it scans them and pre-populates the config with discovered statuses, surfaces, modules, and reference fields.
+
 ## Configuration
 
 Create `dotmd.config.mjs` at your project root (or run `dotmd init`):
 
 ```js
-export const root = 'docs/plans';         // where your .md files live
+export const root = 'docs/plans';         // string or array of paths
 export const archiveDir = 'archived';     // subdirectory for archived docs
 
 export const statuses = {
@@ -312,8 +392,7 @@ export function validate(doc, ctx) {
   const warnings = [];
   if (doc.status === 'active' && !doc.owner) {
     warnings.push({
-      path: doc.path,
-      level: 'warning',
+      path: doc.path, level: 'warning',
       message: 'Active docs should have an owner.',
     });
   }
@@ -332,7 +411,7 @@ export function renderContext(index, defaultRenderer) {
 }
 ```
 
-Available: `renderContext`, `renderCompactList`, `renderCheck`, `renderGraph`, `formatSnapshot`.
+Available: `renderContext`, `renderCompactList`, `renderCheck`, `renderGraph`, `renderStats`, `formatSnapshot`.
 
 ### Lifecycle Hooks
 
@@ -340,33 +419,33 @@ Available: `renderContext`, `renderCompactList`, `renderCheck`, `renderGraph`, `
 export function onArchive(doc, { oldPath, newPath }) {
   console.log(`Archived: ${oldPath} → ${newPath}`);
 }
-
-export function onStatusChange(doc, { oldStatus, newStatus }) {
-  // notify, log, trigger CI, etc.
-}
 ```
 
 Available: `onArchive`, `onStatusChange`, `onTouch`, `onNew`, `onRename`, `onLint`.
 
-### Summarize Hook
-
-Override the diff summarizer (replaces the default MLX model call):
+### AI Hooks
 
 ```js
+// Override doc summarization (replaces local MLX model)
+export function summarizeDoc(body, meta) {
+  return 'Custom summary for ' + meta.title;
+}
+
+// Override diff summarization
 export function summarizeDiff(diffOutput, filePath) {
-  // call your preferred LLM, return a string summary
   return `Changes in ${filePath}: ...`;
 }
 ```
 
 ## Features
 
-- **Zero dependencies** — pure Node.js builtins (`fs`, `path`, `child_process`)
-- **No build step** — ships as plain ESM, runs directly
 - **Git-aware** — detects frontmatter date drift vs git history, uses `git mv` for archives
 - **Dry-run everything** — preview any mutation with `--dry-run` / `-n`
-- **Configurable everything** — statuses, taxonomy, lifecycle, validation rules, display, templates
+- **Multi-root** — manage docs across multiple directories with `--root` filtering
+- **Configurable** — statuses, taxonomy, lifecycle, validation rules, display, templates
 - **Hook system** — extend with JS functions, no plugin framework to learn
+- **AI-powered** — local MLX summaries for docs, queries, diffs, and context briefings
+- **Notion sync** — import, export, and bidirectional sync with Notion databases
 - **LLM-friendly** — `dotmd context` generates compact briefings for AI assistants
 - **Shell completion** — bash and zsh via `dotmd completions`
 

package/bin/dotmd.mjs

@@ -20,6 +20,11 @@ import { runMigrate } from '../src/migrate.mjs';
 import { runFixRefs, fixBrokenRefs } from '../src/fix-refs.mjs';
 import { buildGraph, renderGraphText, renderGraphDot, renderGraphJson } from '../src/graph.mjs';
 import { runDoctor } from '../src/doctor.mjs';
+import { buildStats, renderStats, renderStatsJson } from '../src/stats.mjs';
+import { runSummary } from '../src/summary.mjs';
+import { runDeps } from '../src/deps.mjs';
+import { runExport } from '../src/export.mjs';
+import { runNotion } from '../src/notion.mjs';
 import { die, warn } from '../src/util.mjs';
 
 const __filename = fileURLToPath(import.meta.url);
@@ -34,7 +39,9 @@ Commands:
   json                   Full index as JSON
   check [flags]          Validate frontmatter and references
   coverage [--json]      Metadata coverage report
+  stats [--json]         Doc health dashboard
   graph [--dot|--json]   Visualize document relationships
+  deps [file]            Dependency tree or overview
   context                Compact briefing (LLM-oriented)
   focus [status]         Detailed view for one status group
   query [filters]        Filtered search
@@ -48,8 +55,11 @@ Commands:
   rename <old> <new>     Rename doc and update references
   migrate <f> <old> <new>  Batch update a frontmatter field
   watch [command]       Re-run a command on file changes
+  notion <sub> [db-id]   Notion import/export/sync
+  export [file]          Export docs as md, html, or json
+  summary <file>        AI summary of a document
   diff [file]           Show changes since last updated date
-  new <name>             Create a new document with frontmatter
+  new <name>             Create a new document from template
   init                   Create starter config + docs directory
   completions <shell>    Output shell completion script (bash, zsh)
 
@@ -101,6 +111,14 @@ references in other docs, and regenerates the index.
 
 Use --dry-run (-n) to preview changes without writing anything.`,
 
+  stats: `dotmd stats — doc health dashboard
+
+Shows aggregated metrics: status counts, staleness, errors/warnings,
+freshness, completeness, checklist progress, and audit coverage.
+
+Options:
+  --json                 Machine-readable JSON output`,
+
   graph: `dotmd graph — visualize document relationships
 
 Output formats:
@@ -113,6 +131,18 @@ Filters:
   --module <name>        Show only docs with this module
   --surface <name>       Show only docs with this surface`,
 
+  deps: `dotmd deps [file] — dependency tree or overview
+
+Without a file, shows a flat overview: most blocking docs, most blocked
+docs, docs with blockers, and orphans.
+
+With a file, shows a tree: what the doc depends on (recursive) and what
+depends on it.
+
+Options:
+  --depth <n>            Max tree depth (default: 5)
+  --json                 Machine-readable JSON output`,
+
   doctor: `dotmd doctor — auto-fix everything in one pass
 
 Runs in sequence: fix broken references, lint --fix, sync dates from
@@ -167,6 +197,40 @@ Examples:
   dotmd watch check        # re-run check on changes
   dotmd watch context      # live briefing`,
 
+  notion: `dotmd notion — Notion database integration
+
+Subcommands:
+  import <database-id>   Pull Notion database → local .md files
+  export <database-id>   Push local docs → Notion database rows
+  sync <database-id>     Bidirectional sync (merge by slug)
+
+Options:
+  --force                Overwrite existing files on import
+  --dry-run, -n          Preview without changes
+
+Requires NOTION_TOKEN env var or notion.token in config.`,
+
+  export: `dotmd export — export docs as markdown, HTML, or JSON
+
+Without a file, exports all docs (with optional filters).
+With a file, exports that doc plus all its dependencies.
+
+Options:
+  --format <md|html|json>  Output format (default: md)
+  --output <path>          Write to file/directory (default: stdout for md/json)
+  --status <s1,s2>         Filter by status
+  --module <name>          Filter by module
+  --root <name>            Filter by root`,
+
+  summary: `dotmd summary <file> — AI summary of a document
+
+Generates an AI-powered summary using a local MLX model via uv.
+
+Options:
+  --model <name>         MLX model (default: mlx-community/Llama-3.2-3B-Instruct-4bit)
+  --max-tokens <n>       Max tokens for generation (default: 200)
+  --json                 Output as JSON`,
+
   diff: `dotmd diff [file] — show changes since last updated date
 
 Shows git diffs for docs that changed after their frontmatter updated date.
@@ -270,7 +334,8 @@ async function main() {
 
   if (verbose) {
     process.stderr.write(`Config: ${config.configPath ?? 'none'}\n`);
-    process.stderr.write(`Docs root: ${config.docsRoot}\n`);
+    const roots = config.docsRoots || [config.docsRoot];
+    process.stderr.write(`Docs root${roots.length > 1 ? 's' : ''}: ${roots.join(', ')}\n`);
     process.stderr.write(`Repo root: ${config.repoRoot}\n`);
   }
 
@@ -284,6 +349,10 @@ async function main() {
   // Watch and diff (handle their own index building)
   if (command === 'watch') { runWatch(restArgs, config); return; }
   if (command === 'diff') { runDiff(restArgs, config); return; }
+  if (command === 'summary') { runSummary(restArgs, config); return; }
+  if (command === 'deps') { runDeps(restArgs, config); return; }
+  if (command === 'export') { runExport(restArgs, config); return; }
+  if (command === 'notion') { await runNotion(restArgs, config, { dryRun }); return; }
 
   // Lifecycle commands
   if (command === 'status') { runStatus(restArgs, config, { dryRun }); return; }
@@ -298,6 +367,17 @@ async function main() {
 
   const index = buildIndex(config);
 
+  // Apply --root filter
+  const rootFilter = (() => { const i = args.indexOf('--root'); return i !== -1 && args[i + 1] ? args[i + 1] : null; })();
+  if (rootFilter) {
+    index.docs = index.docs.filter(d => d.root === rootFilter || d.root.endsWith('/' + rootFilter) || d.root.split('/').pop() === rootFilter);
+    index.errors = index.errors.filter(e => index.docs.some(d => d.path === e.path));
+    index.warnings = index.warnings.filter(w => index.docs.some(d => d.path === w.path));
+    for (const status of config.statusOrder) {
+      index.countsByStatus[status] = index.docs.filter(d => d.status === status).length;
+    }
+  }
+
   if (verbose) {
     process.stderr.write(`Docs found: ${index.docs.length}\n`);
   }
@@ -353,6 +433,16 @@ async function main() {
     return;
   }
 
+  if (command === 'stats') {
+    const stats = buildStats(index, config);
+    if (args.includes('--json')) {
+      process.stdout.write(renderStatsJson(stats));
+    } else {
+      process.stdout.write(renderStats(stats, config));
+    }
+    return;
+  }
+
   if (command === 'index') {
     if (!config.indexPath) {
       die('Index generation is not configured. Add an `index` section to your dotmd.config.mjs.');
@@ -372,7 +462,13 @@ async function main() {
 
   if (command === 'focus') { runFocus(index, restArgs, config); return; }
   if (command === 'query') { runQuery(index, restArgs, config); return; }
-  if (command === 'context') { process.stdout.write(renderContext(index, config)); return; }
+  if (command === 'context') {
+    const summarize = args.includes('--summarize');
+    const modelIdx = args.indexOf('--model');
+    const model = modelIdx !== -1 && args[modelIdx + 1] ? args[modelIdx + 1] : undefined;
+    process.stdout.write(renderContext(index, config, { summarize, model }));
+    return;
+  }
 
   if (command === 'graph') {
     const statusFilter = (() => { const i = args.indexOf('--status'); return i !== -1 && args[i + 1] ? args[i + 1] : null; })();

package/package.json

@@ -1,7 +1,7 @@
 {
   "name": "dotmd-cli",
-  "version": "0.7.6",
-  "description": "CLI for managing markdown documents with YAML frontmatter — index, query, validate, lifecycle.",
+  "version": "0.8.0",
+  "description": "CLI for managing markdown documents with YAML frontmatter — index, query, validate, graph, export, Notion sync, AI summaries.",
   "type": "module",
   "license": "MIT",
   "bin": {
@@ -24,16 +24,27 @@
     "adr",
     "rfc",
     "document-management",
-    "yaml"
+    "yaml",
+    "notion",
+    "graph",
+    "export",
+    "ai-summary",
+    "validation",
+    "lifecycle"
   ],
   "repository": {
     "type": "git",
     "url": "git+https://github.com/reowens/dotmd.git"
   },
+  "homepage": "https://github.com/reowens/dotmd#readme",
   "scripts": {
     "test": "node --test test/*.test.mjs"
   },
   "engines": {
     "node": ">=18"
+  },
+  "dependencies": {
+    "@notionhq/client": "^5.13.0",
+    "notion-to-md": "^3.1.9"
   }
 }

package/src/ai.mjs

@@ -0,0 +1,50 @@
+import { spawnSync } from 'node:child_process';
+import { warn } from './util.mjs';
+
+let uvChecked = null;
+
+export function checkUvAvailable() {
+  if (uvChecked !== null) return uvChecked;
+  const result = spawnSync('uv', ['--version'], { encoding: 'utf8' });
+  uvChecked = !result.error && result.status === 0;
+  if (!uvChecked) warn('uv is not installed. Install it to enable AI summaries: https://docs.astral.sh/uv/');
+  return uvChecked;
+}
+
+export function runMLX(prompt, opts = {}) {
+  const { model = 'mlx-community/Llama-3.2-3B-Instruct-4bit', maxTokens = 200, timeout = 120000 } = opts;
+  if (!checkUvAvailable()) return null;
+
+  const result = spawnSync('uv', [
+    'run', '--with', 'mlx-lm',
+    'python3', '-m', 'mlx_lm', 'generate',
+    '--model', model,
+    '--prompt', prompt,
+    '--max-tokens', String(maxTokens),
+    '--verbose', 'false',
+  ], { encoding: 'utf8', timeout });
+
+  if (result.status !== 0) return null;
+
+  const output = result.stdout.trim();
+  const lines = output.split('\n')
+    .filter(l => !l.includes('Fetching') && !l.includes('Warning:') && !l.includes('=========='));
+  return lines.join(' ').trim() || null;
+}
+
+export function summarizeDocBody(bodyText, meta, opts = {}) {
+  if (!bodyText?.trim()) return null;
+  const prompt = `Summarize this markdown document in 2-3 sentences. Focus on what the document is about, its current state, and any key next actions or open questions.
+
+Title: ${meta.title}
+Status: ${meta.status}
+File: ${meta.path}
+
+${bodyText.slice(0, 6000)}`;
+  return runMLX(prompt, { maxTokens: 200, ...opts });
+}
+
+export function summarizeDiffText(diffText, filePath, model) {
+  const prompt = `Summarize this git diff in 1-2 sentences. Focus on what changed semantically, not line counts.\n\nFile: ${filePath}\n\n${diffText.slice(0, 4000)}`;
+  return runMLX(prompt, { model, maxTokens: 150 });
+}

package/src/completions.mjs

@@ -1,28 +1,35 @@
 import { die } from './util.mjs';
 
 const COMMANDS = [
-  'list', 'json', 'check', 'coverage', 'graph', 'context', 'focus', 'query',
+  'list', 'json', 'check', 'coverage', 'stats', 'graph', 'deps', 'context', 'focus', 'query',
   'index', 'status', 'archive', 'touch', 'doctor', 'lint', 'rename', 'migrate',
-  'fix-refs', 'watch', 'diff', 'init', 'new', 'completions',
+  'fix-refs', 'notion', 'export', 'summary', 'watch', 'diff', 'init', 'new', 'completions',
 ];
 
-const GLOBAL_FLAGS = ['--config', '--dry-run', '--verbose', '--help', '--version'];
+const GLOBAL_FLAGS = ['--config', '--dry-run', '--verbose', '--root', '--help', '--version'];
 
 const COMMAND_FLAGS = {
   query: ['--status', '--keyword', '--module', '--surface', '--domain', '--owner',
           '--updated-since', '--stale', '--has-next-step', '--has-blockers',
-          '--checklist-open', '--sort', '--limit', '--all', '--git', '--json'],
+          '--checklist-open', '--sort', '--limit', '--all', '--git', '--json',
+          '--summarize', '--summarize-limit', '--model'],
   index: ['--write'],
   list: ['--verbose'],
   coverage: ['--json'],
-  new: ['--status', '--title', '--template', '--list-templates'],
+  new: ['--status', '--title', '--template', '--list-templates', '--root'],
   diff: ['--stat', '--since', '--summarize', '--model'],
   check: ['--errors-only', '--fix'],
+  stats: ['--json'],
   graph: ['--dot', '--json', '--status', '--module', '--surface'],
+  deps: ['--json', '--depth'],
+  notion: ['import', 'export', 'sync', '--force', '--dry-run'],
+  export: ['--format', '--output', '--status', '--module', '--root'],
   lint: ['--fix'],
   rename: [],
   migrate: [],
   'fix-refs': [],
+  summary: ['--model', '--max-tokens', '--json'],
+  context: ['--summarize', '--model'],
   touch: ['--git'],
 };
 

package/src/config.mjs

@@ -57,6 +57,8 @@ const DEFAULTS = {
 
   templates: {},
 
+  notion: null,
+
   presets: {
     stale: ['--status', 'active,ready,planned,blocked,research', '--stale', '--sort', 'updated', '--all'],
     actionable: ['--status', 'active,ready', '--has-next-step', '--sort', 'updated', '--all'],
@@ -182,11 +184,15 @@ export async function resolveConfig(cwd, explicitConfigPath) {
 
   const config = deepMerge(DEFAULTS, userConfig);
 
-  const docsRoot = path.resolve(configDir, config.root);
+  const rootPaths = Array.isArray(config.root) ? config.root : [config.root];
+  const docsRoots = rootPaths.map(r => path.resolve(configDir, r));
+  const docsRoot = docsRoots[0]; // primary root for backwards compat
 
   const earlyWarnings = [];
-  if (!existsSync(docsRoot)) {
-    earlyWarnings.push('Config: docs root does not exist: ' + docsRoot);
+  for (const dr of docsRoots) {
+    if (!existsSync(dr)) {
+      earlyWarnings.push('Config: docs root does not exist: ' + dr);
+    }
   }
 
   // Find repo root by walking up looking for .git
@@ -235,6 +241,7 @@ export async function resolveConfig(cwd, explicitConfigPath) {
     raw: config,
 
     docsRoot,
+    docsRoots,
     repoRoot,
     configDir,
     configPath: configPath ?? null,