@bookedsolid/reagent 0.14.0 → 0.14.3

package/dist/cli/commands/obsidian.js

@@ -0,0 +1,187 @@
+import { VaultWriter } from '../../obsidian/vault-writer.js';
+import { ObsidianCli } from '../../obsidian/cli.js';
+import { parseFlag } from '../utils.js';
+const VALID_TARGETS = ['kanban', 'context', 'wiki', 'tasks'];
+export function runObsidian(args) {
+    const subcommand = args[0];
+    if (!subcommand || subcommand === 'help' || subcommand === '--help') {
+        printObsidianHelp();
+        return;
+    }
+    switch (subcommand) {
+        case 'sync':
+            runObsidianSync(args.slice(1));
+            break;
+        case 'status':
+            runObsidianStatus();
+            break;
+        case 'health':
+            runObsidianHealth();
+            break;
+        case 'journal':
+            runObsidianJournal();
+            break;
+        default:
+            console.error(`Unknown obsidian subcommand: ${subcommand}`);
+            printObsidianHelp();
+            process.exit(1);
+    }
+}
+function runObsidianSync(args) {
+    const dryRun = args.includes('--dry-run');
+    const targetFlag = parseFlag(args, '--target');
+    if (targetFlag && !VALID_TARGETS.includes(targetFlag)) {
+        console.error(`Invalid sync target: ${targetFlag}`);
+        console.error(`Valid targets: ${VALID_TARGETS.join(', ')}`);
+        process.exit(1);
+    }
+    const writer = new VaultWriter(process.cwd());
+    if (!writer.isEnabled()) {
+        console.log('Obsidian vault integration is not configured or disabled.');
+        console.log('');
+        console.log('To enable:');
+        console.log('  1. Set REAGENT_OBSIDIAN_VAULT env var to your vault path');
+        console.log('  2. Run: reagent init --obsidian');
+        console.log('  3. Set obsidian_vault.enabled: true in .reagent/gateway.yaml');
+        return;
+    }
+    if (dryRun) {
+        console.log('Dry run — no files will be written.\n');
+    }
+    if (targetFlag) {
+        const result = targetFlag === 'kanban'
+            ? writer.syncKanban(dryRun)
+            : targetFlag === 'context'
+                ? writer.syncContextDump(dryRun)
+                : targetFlag === 'wiki'
+                    ? writer.syncWiki(dryRun)
+                    : writer.syncTasks(dryRun);
+        printSyncResult(result);
+    }
+    else {
+        const results = writer.syncAll(dryRun);
+        for (const result of results) {
+            printSyncResult(result);
+        }
+    }
+}
+function runObsidianStatus() {
+    const writer = new VaultWriter(process.cwd());
+    const config = writer.getConfig();
+    if (!config) {
+        console.log('Obsidian vault: not configured');
+        return;
+    }
+    console.log('Obsidian vault: enabled');
+    console.log(`  Vault path: ${config.vault_path}`);
+    if (config.vault_name) {
+        console.log(`  Vault name: ${config.vault_name}`);
+    }
+    // CLI availability
+    const cliAvailable = ObsidianCli.isAvailable();
+    console.log(`  Obsidian CLI: ${cliAvailable ? 'available' : 'not found'}`);
+    console.log('  Paths:');
+    console.log(`    root:     ${config.paths.root}`);
+    console.log(`    kanban:   ${config.paths.kanban}`);
+    console.log(`    sources:  ${config.paths.sources}`);
+    console.log(`    wiki:     ${config.paths.wiki}`);
+    console.log(`    tasks:    ${config.paths.tasks}`);
+    console.log(`    sessions: ${config.paths.sessions}`);
+    console.log('  Sync targets:');
+    console.log(`    kanban:       ${config.sync.kanban ? 'enabled' : 'disabled'}`);
+    console.log(`    context_dump: ${config.sync.context_dump ? 'enabled' : 'disabled'}`);
+    console.log(`    wiki_refresh: ${config.sync.wiki_refresh ? 'enabled' : 'disabled'}`);
+    console.log(`    journal:      ${config.sync.journal ? 'enabled' : 'disabled'}`);
+    console.log(`    precompact:   ${config.sync.precompact ? 'enabled' : 'disabled'}`);
+    console.log(`    tasks:        ${config.sync.tasks ? 'enabled' : 'disabled'}`);
+}
+function runObsidianHealth() {
+    const writer = new VaultWriter(process.cwd());
+    const config = writer.getConfig();
+    if (!config) {
+        console.log('Obsidian vault: not configured');
+        return;
+    }
+    if (!ObsidianCli.isAvailable()) {
+        console.log('Obsidian CLI not found at /usr/local/bin/obsidian');
+        return;
+    }
+    if (!config.vault_name) {
+        console.log('vault_name not set in gateway.yaml — required for CLI commands');
+        return;
+    }
+    const cli = new ObsidianCli(config.vault_name);
+    const health = cli.vaultHealth();
+    if (!health) {
+        console.log('Failed to get vault health metrics');
+        return;
+    }
+    console.log(`Vault health — ${config.vault_name}:`);
+    console.log(`  Orphans:    ${health.orphans}`);
+    console.log(`  Unresolved: ${health.unresolved}`);
+    console.log(`  Dead ends:  ${health.deadends}`);
+}
+function runObsidianJournal() {
+    const writer = new VaultWriter(process.cwd());
+    const config = writer.getConfig();
+    if (!config) {
+        console.log('Obsidian vault: not configured');
+        return;
+    }
+    if (!ObsidianCli.isAvailable()) {
+        console.log('Obsidian CLI not found at /usr/local/bin/obsidian');
+        return;
+    }
+    if (!config.vault_name) {
+        console.log('vault_name not set in gateway.yaml — required for CLI commands');
+        return;
+    }
+    if (!config.sync.journal) {
+        console.log('Journal sync not enabled in gateway.yaml');
+        return;
+    }
+    const cli = new ObsidianCli(config.vault_name);
+    const projectName = process.cwd().split('/').pop() || 'unknown';
+    const timestamp = new Date().toISOString().replace('T', ' ').slice(0, 16);
+    const content = `### ${projectName} — Manual journal entry (${timestamp})\n\n- Triggered via \`reagent obsidian journal\`\n\n---\n`;
+    const success = cli.dailyAppend(content);
+    if (success) {
+        console.log('Session journal entry appended to daily note');
+    }
+    else {
+        console.log('Failed to append journal entry');
+    }
+}
+function printSyncResult(result) {
+    if (result.written) {
+        console.log(`  [synced] ${result.target} → ${result.path}`);
+    }
+    else if (result.error) {
+        console.log(`  [skip]   ${result.target}: ${result.error}`);
+    }
+    else {
+        console.log(`  [skip]   ${result.target}: not configured`);
+    }
+}
+function printObsidianHelp() {
+    console.log(`
+reagent obsidian — Obsidian vault integration
+
+Usage:
+  reagent obsidian sync [--target kanban|context|wiki|tasks] [--dry-run]
+  reagent obsidian status
+  reagent obsidian health
+  reagent obsidian journal
+
+Commands:
+  sync     Sync enabled targets to the Obsidian vault
+  status   Show current Obsidian configuration and CLI availability
+  health   Show vault health metrics (orphans, unresolved links, dead ends)
+  journal  Manually trigger a session journal entry in the daily note
+
+Options:
+  --target <name>   Sync a specific target only (kanban, context, wiki, tasks)
+  --dry-run         Preview what would be written without writing files
+`);
+}
+//# sourceMappingURL=obsidian.js.map

package/dist/cli/commands/obsidian.js.map

@@ -0,0 +1 @@
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package/dist/cli/commands/upgrade-policy.d.ts

@@ -0,0 +1,17 @@
+import type { InstallResult } from './init/types.js';
+/**
+ * YAML-aware policy merge for `reagent upgrade`.
+ *
+ * Uses the `yaml` package's `parseDocument` API to preserve
+ * comments, ordering, and existing user customizations.
+ *
+ * Behavior:
+ *   1. Parse existing policy.yaml as a YAML Document
+ *   2. Add missing top-level sections (shallow merge — never overwrites existing)
+ *   3. Update `installed_by` version stamp
+ *   4. If `cleanBlockedPaths`: replace `.reagent/` with granular entries
+ */
+export declare function mergePolicy(targetDir: string, pkgVersion: string, dryRun: boolean, options?: {
+    cleanBlockedPaths?: boolean;
+}): InstallResult[];
+//# sourceMappingURL=upgrade-policy.d.ts.map

package/dist/cli/commands/upgrade-policy.d.ts.map

@@ -0,0 +1 @@
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package/dist/cli/commands/upgrade-policy.js

@@ -0,0 +1,123 @@
+import fs from 'node:fs';
+import path from 'node:path';
+import { parseDocument } from 'yaml';
+/**
+ * Canonical sections that should exist in every policy.yaml.
+ * mergePolicy adds these if missing — never overwrites existing values.
+ */
+const CANONICAL_SECTIONS = {
+    context_protection: {
+        delegate_to_subagent: ['pnpm run preflight', 'pnpm run test', 'pnpm run build'],
+        max_bash_output_lines: 100,
+    },
+};
+/**
+ * Granular blocked_paths that replace the blanket `.reagent/` entry.
+ */
+const GRANULAR_BLOCKED_PATHS = ['.reagent/policy.yaml', '.reagent/HALT'];
+/**
+ * YAML-aware policy merge for `reagent upgrade`.
+ *
+ * Uses the `yaml` package's `parseDocument` API to preserve
+ * comments, ordering, and existing user customizations.
+ *
+ * Behavior:
+ *   1. Parse existing policy.yaml as a YAML Document
+ *   2. Add missing top-level sections (shallow merge — never overwrites existing)
+ *   3. Update `installed_by` version stamp
+ *   4. If `cleanBlockedPaths`: replace `.reagent/` with granular entries
+ */
+export function mergePolicy(targetDir, pkgVersion, dryRun, options) {
+    const policyPath = path.join(targetDir, '.reagent', 'policy.yaml');
+    const results = [];
+    if (!fs.existsSync(policyPath)) {
+        results.push({ file: '.reagent/policy.yaml', status: 'warn' });
+        console.warn('  Warning: .reagent/policy.yaml not found. Run `reagent init` to create it.');
+        return results;
+    }
+    const raw = fs.readFileSync(policyPath, 'utf8');
+    const doc = parseDocument(raw);
+    // Guard: empty or malformed YAML (no mapping node)
+    if (!doc.contents) {
+        results.push({ file: '.reagent/policy.yaml', status: 'warn' });
+        console.warn('  Warning: .reagent/policy.yaml is empty or malformed. Run `reagent init` to recreate.');
+        return results;
+    }
+    let changed = false;
+    // 1. Update installed_by version stamp
+    const currentVersion = doc.get('installed_by');
+    const newVersion = `reagent@${pkgVersion}`;
+    if (currentVersion !== newVersion) {
+        doc.set('installed_by', newVersion);
+        changed = true;
+    }
+    // 2. Add missing canonical sections (shallow — never overwrite existing)
+    for (const [key, value] of Object.entries(CANONICAL_SECTIONS)) {
+        if (!doc.has(key)) {
+            doc.set(key, value);
+            changed = true;
+            results.push({
+                file: `.reagent/policy.yaml (added ${key} section)`,
+                status: 'installed',
+            });
+        }
+    }
+    // 3. Clean blocked_paths if requested
+    if (options?.cleanBlockedPaths) {
+        // doc.get() on a parseDocument returns YAML AST nodes, not plain arrays.
+        // Use toJSON() to resolve to plain JS values for manipulation.
+        const blockedNode = doc.get('blocked_paths');
+        if (blockedNode != null) {
+            const values = typeof blockedNode.toJSON === 'function'
+                ? blockedNode.toJSON()
+                : Array.isArray(blockedNode)
+                    ? blockedNode
+                    : [];
+            if (Array.isArray(values)) {
+                const hasReagentBlanket = values.some((v) => v === '.reagent/' || v === '.reagent');
+                if (hasReagentBlanket) {
+                    const cleaned = values.filter((v) => v !== '.reagent/' && v !== '.reagent');
+                    for (const granular of GRANULAR_BLOCKED_PATHS) {
+                        if (!cleaned.includes(granular)) {
+                            cleaned.push(granular);
+                        }
+                    }
+                    doc.set('blocked_paths', cleaned);
+                    changed = true;
+                    results.push({
+                        file: '.reagent/policy.yaml (blocked_paths: .reagent/ → granular)',
+                        status: 'updated',
+                    });
+                }
+            }
+        }
+    }
+    // 4. Write or report
+    if (changed) {
+        if (!dryRun) {
+            try {
+                fs.writeFileSync(policyPath, doc.toString(), 'utf8');
+            }
+            catch {
+                results.push({ file: '.reagent/policy.yaml', status: 'warn' });
+                console.warn('  Warning: .reagent/policy.yaml has YAML errors and cannot be updated.');
+                return results;
+            }
+            results.push({
+                file: '.reagent/policy.yaml (installed_by updated)',
+                status: 'updated',
+            });
+        }
+        else {
+            results.push({
+                file: '.reagent/policy.yaml (installed_by would be updated)',
+                status: 'updated',
+            });
+        }
+    }
+    else {
+        results.push({ file: '.reagent/policy.yaml', status: 'skipped' });
+    }
+    return results;
+}
+//# sourceMappingURL=upgrade-policy.js.map

package/dist/cli/commands/upgrade-policy.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"upgrade-policy.js","sourceRoot":"","sources":["../../../src/cli/commands/upgrade-policy.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,MAAM,SAAS,CAAC;AACzB,OAAO,IAAI,MAAM,WAAW,CAAC;AAC7B,OAAO,EAAE,aAAa,EAAE,MAAM,MAAM,CAAC;AAGrC;;;GAGG;AACH,MAAM,kBAAkB,GAA4B;IAClD,kBAAkB,EAAE;QAClB,oBAAoB,EAAE,CAAC,oBAAoB,EAAE,eAAe,EAAE,gBAAgB,CAAC;QAC/E,qBAAqB,EAAE,GAAG;KAC3B;CACF,CAAC;AAEF;;GAEG;AACH,MAAM,sBAAsB,GAAG,CAAC,sBAAsB,EAAE,eAAe,CAAC,CAAC;AAEzE;;;;;;;;;;;GAWG;AACH,MAAM,UAAU,WAAW,CACzB,SAAiB,EACjB,UAAkB,EAClB,MAAe,EACf,OAAyC;IAEzC,MAAM,UAAU,GAAG,IAAI,CAAC,IAAI,CAAC,SAAS,EAAE,UAAU,EAAE,aAAa,CAAC,CAAC;IACnE,MAAM,OAAO,GAAoB,EAAE,CAAC;IAEpC,IAAI,CAAC,EAAE,CAAC,UAAU,CAAC,UAAU,CAAC,EAAE,CAAC;QAC/B,OAAO,CAAC,IAAI,CAAC,EAAE,IAAI,EAAE,sBAAsB,EAAE,MAAM,EAAE,MAAM,EAAE,CAAC,CAAC;QAC/D,OAAO,CAAC,IAAI,CAAC,6EAA6E,CAAC,CAAC;QAC5F,OAAO,OAAO,CAAC;IACjB,CAAC;IAED,MAAM,GAAG,GAAG,EAAE,CAAC,YAAY,CAAC,UAAU,EAAE,MAAM,CAAC,CAAC;IAChD,MAAM,GAAG,GAAG,aAAa,CAAC,GAAG,CAAC,CAAC;IAE/B,mDAAmD;IACnD,IAAI,CAAC,GAAG,CAAC,QAAQ,EAAE,CAAC;QAClB,OAAO,CAAC,IAAI,CAAC,EAAE,IAAI,EAAE,sBAAsB,EAAE,MAAM,EAAE,MAAM,EAAE,CAAC,CAAC;QAC/D,OAAO,CAAC,IAAI,CACV,wFAAwF,CACzF,CAAC;QACF,OAAO,OAAO,CAAC;IACjB,CAAC;IAED,IAAI,OAAO,GAAG,KAAK,CAAC;IAEpB,uCAAuC;IACvC,MAAM,cAAc,GAAG,GAAG,CAAC,GAAG,CAAC,cAAc,CAAuB,CAAC;IACrE,MAAM,UAAU,GAAG,WAAW,UAAU,EAAE,CAAC;IAC3C,IAAI,cAAc,KAAK,UAAU,EAAE,CAAC;QAClC,GAAG,CAAC,GAAG,CAAC,cAAc,EAAE,UAAU,CAAC,CAAC;QACpC,OAAO,GAAG,IAAI,CAAC;IACjB,CAAC;IAED,yEAAyE;IACzE,KAAK,MAAM,CAAC,GAAG,EAAE,KAAK,CAAC,IAAI,MAAM,CAAC,OAAO,CAAC,kBAAkB,CAAC,EAAE,CAAC;QAC9D,IAAI,CAAC,GAAG,CAAC,GAAG,CAAC,GAAG,CAAC,EAAE,CAAC;YAClB,GAAG,CAAC,GAAG,CAAC,GAAG,EAAE,KAAK,CAAC,CAAC;YACpB,OAAO,GAAG,IAAI,CAAC;YACf,OAAO,CAAC,IAAI,CAAC;gBACX,IAAI,EAAE,+BAA+B,GAAG,WAAW;gBACnD,MAAM,EAAE,WAAW;aACpB,CAAC,CAAC;QACL,CAAC;IACH,CAAC;IAED,sCAAsC;IACtC,IAAI,OAAO,EAAE,iBAAiB,EAAE,CAAC;QAC/B,yEAAyE;QACzE,+DAA+D;QAC/D,MAAM,WAAW,GAAG,GAAG,CAAC,GAAG,CAAC,eAAe,CAAC,CAAC;QAC7C,IAAI,WAAW,IAAI,IAAI,EAAE,CAAC;YACxB,MAAM,MAAM,GACV,OAAQ,WAA0C,CAAC,MAAM,KAAK,UAAU;gBACtE,CAAC,CAAG,WAAyC,CAAC,MAAM,EAAgB;gBACpE,CAAC,CAAC,KAAK,CAAC,OAAO,CAAC,WAAW,CAAC;oBAC1B,CAAC,CAAC,WAAW;oBACb,CAAC,CAAC,EAAE,CAAC;YAEX,IAAI,KAAK,CAAC,OAAO,CAAC,MAAM,CAAC,EAAE,CAAC;gBAC1B,MAAM,iBAAiB,GAAG,MAAM,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,KAAK,WAAW,IAAI,CAAC,KAAK,UAAU,CAAC,CAAC;gBACpF,IAAI,iBAAiB,EAAE,CAAC;oBACtB,MAAM,OAAO,GAAG,MAAM,CAAC,MAAM,CAAC,CAAC,CAAU,EAAE,EAAE,CAAC,CAAC,KAAK,WAAW,IAAI,CAAC,KAAK,UAAU,CAAC,CAAC;oBACrF,KAAK,MAAM,QAAQ,IAAI,sBAAsB,EAAE,CAAC;wBAC9C,IAAI,CAAC,OAAO,CAAC,QAAQ,CAAC,QAAQ,CAAC,EAAE,CAAC;4BAChC,OAAO,CAAC,IAAI,CAAC,QAAQ,CAAC,CAAC;wBACzB,CAAC;oBACH,CAAC;oBACD,GAAG,CAAC,GAAG,CAAC,eAAe,EAAE,OAAO,CAAC,CAAC;oBAClC,OAAO,GAAG,IAAI,CAAC;oBACf,OAAO,CAAC,IAAI,CAAC;wBACX,IAAI,EAAE,4DAA4D;wBAClE,MAAM,EAAE,SAAS;qBAClB,CAAC,CAAC;gBACL,CAAC;YACH,CAAC;QACH,CAAC;IACH,CAAC;IAED,qBAAqB;IACrB,IAAI,OAAO,EAAE,CAAC;QACZ,IAAI,CAAC,MAAM,EAAE,CAAC;YACZ,IAAI,CAAC;gBACH,EAAE,CAAC,aAAa,CAAC,UAAU,EAAE,GAAG,CAAC,QAAQ,EAAE,EAAE,MAAM,CAAC,CAAC;YACvD,CAAC;YAAC,MAAM,CAAC;gBACP,OAAO,CAAC,IAAI,CAAC,EAAE,IAAI,EAAE,sBAAsB,EAAE,MAAM,EAAE,MAAM,EAAE,CAAC,CAAC;gBAC/D,OAAO,CAAC,IAAI,CAAC,wEAAwE,CAAC,CAAC;gBACvF,OAAO,OAAO,CAAC;YACjB,CAAC;YACD,OAAO,CAAC,IAAI,CAAC;gBACX,IAAI,EAAE,6CAA6C;gBACnD,MAAM,EAAE,SAAS;aAClB,CAAC,CAAC;QACL,CAAC;aAAM,CAAC;YACN,OAAO,CAAC,IAAI,CAAC;gBACX,IAAI,EAAE,sDAAsD;gBAC5D,MAAM,EAAE,SAAS;aAClB,CAAC,CAAC;QACL,CAAC;IACH,CAAC;SAAM,CAAC;QACN,OAAO,CAAC,IAAI,CAAC,EAAE,IAAI,EAAE,sBAAsB,EAAE,MAAM,EAAE,SAAS,EAAE,CAAC,CAAC;IACpE,CAAC;IAED,OAAO,OAAO,CAAC;AACjB,CAAC"}

package/dist/cli/commands/upgrade.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"upgrade.d.ts","sourceRoot":"","sources":["../../../src/cli/commands/upgrade.ts"],"names":[],"mappings":"AAaA,wBAAgB,UAAU,CAAC,IAAI,EAAE,MAAM,EAAE,GAAG,IAAI,CA0E/C"}
+{"version":3,"file":"upgrade.d.ts","sourceRoot":"","sources":["../../../src/cli/commands/upgrade.ts"],"names":[],"mappings":"AAcA,wBAAgB,UAAU,CAAC,IAAI,EAAE,MAAM,EAAE,GAAG,IAAI,CA2D/C"}

package/dist/cli/commands/upgrade.js

@@ -2,6 +2,7 @@ import fs from 'node:fs';
 import path from 'node:path';
 import { PKG_ROOT, getPkgVersion } from '../utils.js';
 import { installHuskyHook } from './init/husky-hooks.js';
+import { mergePolicy } from './upgrade-policy.js';
 // All hook names managed by reagent, mapped to their source file names
 const HOOK_MAP = [
     { hookName: 'commit-msg', srcFileName: 'commit-msg.sh' },
@@ -11,6 +12,7 @@ const HOOK_MAP = [
 export function runUpgrade(args) {
     const targetDir = process.cwd();
     const dryRun = args.includes('--dry-run');
+    const cleanBlockedPaths = args.includes('--clean-blocked-paths');
     const PKG_VERSION = getPkgVersion();
     console.log(`\n@bookedsolid/reagent v${PKG_VERSION} upgrade`);
     console.log(`  Target: ${targetDir}`);
@@ -42,33 +44,62 @@ export function runUpgrade(args) {
         const hookResults = installHuskyHook(targetDir, hookName, srcFileName, dryRun);
         results.push(...hookResults);
     }
-    // Step 2: Update installed_by in .reagent/policy.yaml to reflect current version.
-    // Only touches the installed_by line — all other user config is preserved.
-    const policyPath = path.join(targetDir, '.reagent', 'policy.yaml');
-    if (!fs.existsSync(policyPath)) {
-        results.push({ file: '.reagent/policy.yaml', status: 'warn' });
-        console.warn('  Warning: .reagent/policy.yaml not found. Run `reagent init` to create it.');
+    // Step 2: YAML-aware policy merge — updates version stamp, adds missing
+    // canonical sections, and optionally cleans blocked_paths.
+    const policyResults = mergePolicy(targetDir, PKG_VERSION, dryRun, {
+        cleanBlockedPaths,
+    });
+    results.push(...policyResults);
+    // Step 3: Fix .mcp.json if it uses the broken npx pattern.
+    // pnpm projects don't get node_modules/.bin/reagent, so npx fails.
+    // Migrate to the direct node path which works across all package managers.
+    const mcpResults = upgradeMcpJson(targetDir, dryRun);
+    results.push(...mcpResults);
+    printSummary(results, dryRun);
+}
+/**
+ * Fix .mcp.json if it uses the broken npx pattern.
+ * Migrates to `node node_modules/@bookedsolid/reagent/dist/cli/index.js serve`
+ * which works across npm, yarn, pnpm, and bun.
+ */
+function upgradeMcpJson(targetDir, dryRun) {
+    const mcpPath = path.join(targetDir, '.mcp.json');
+    if (!fs.existsSync(mcpPath)) {
+        return [];
     }
-    else {
-        const policyContent = fs.readFileSync(policyPath, 'utf8');
-        const updatedContent = policyContent.replace(/^installed_by:\s*['"]?reagent@[^'">\n]+['"]?/m, `installed_by: 'reagent@${PKG_VERSION}'`);
-        if (updatedContent === policyContent) {
-            // Line didn't match the expected pattern — still show as skipped, don't corrupt the file
-            results.push({ file: '.reagent/policy.yaml', status: 'skipped' });
-        }
-        else if (!dryRun) {
-            fs.writeFileSync(policyPath, updatedContent, 'utf8');
-            results.push({ file: '.reagent/policy.yaml (installed_by updated)', status: 'updated' });
-        }
-        else {
-            // dry-run: report what would change
-            results.push({
-                file: '.reagent/policy.yaml (installed_by would be updated)',
-                status: 'updated',
-            });
-        }
+    let config;
+    try {
+        config = JSON.parse(fs.readFileSync(mcpPath, 'utf8'));
     }
-    printSummary(results, dryRun);
+    catch {
+        return [{ file: '.mcp.json', status: 'warn' }];
+    }
+    const entry = config.mcpServers?.reagent;
+    if (!entry)
+        return [];
+    // Check if it's using the broken npx pattern
+    const isNpx = entry.command === 'npx' &&
+        Array.isArray(entry.args) &&
+        entry.args.some((a) => a === 'reagent' || a === '@bookedsolid/reagent');
+    if (!isNpx)
+        return [{ file: '.mcp.json', status: 'skipped' }];
+    // Check if the local dist CLI exists
+    const localCli = path.join(targetDir, 'node_modules', '@bookedsolid', 'reagent', 'dist', 'cli', 'index.js');
+    if (!fs.existsSync(localCli)) {
+        return [{ file: '.mcp.json', status: 'skipped' }];
+    }
+    // Migrate to node direct path
+    entry.command = 'node';
+    entry.args = ['node_modules/@bookedsolid/reagent/dist/cli/index.js', 'serve'];
+    if (!dryRun) {
+        fs.writeFileSync(mcpPath, JSON.stringify(config, null, 2) + '\n');
+    }
+    return [
+        {
+            file: '.mcp.json (migrated npx → node for pnpm compatibility)',
+            status: 'updated',
+        },
+    ];
 }
 function printSummary(results, dryRun) {
     console.log('');

package/dist/cli/commands/upgrade.js.map

@@ -1 +1 @@
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+{"version":3,"file":"upgrade.js","sourceRoot":"","sources":["../../../src/cli/commands/upgrade.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,MAAM,SAAS,CAAC;AACzB,OAAO,IAAI,MAAM,WAAW,CAAC;AAC7B,OAAO,EAAE,QAAQ,EAAE,aAAa,EAAE,MAAM,aAAa,CAAC;AAEtD,OAAO,EAAE,gBAAgB,EAAE,MAAM,uBAAuB,CAAC;AACzD,OAAO,EAAE,WAAW,EAAE,MAAM,qBAAqB,CAAC;AAElD,uEAAuE;AACvE,MAAM,QAAQ,GAAqD;IACjE,EAAE,QAAQ,EAAE,YAAY,EAAE,WAAW,EAAE,eAAe,EAAE;IACxD,EAAE,QAAQ,EAAE,YAAY,EAAE,WAAW,EAAE,eAAe,EAAE;IACxD,EAAE,QAAQ,EAAE,UAAU,EAAE,WAAW,EAAE,aAAa,EAAE;CACrD,CAAC;AAEF,MAAM,UAAU,UAAU,CAAC,IAAc;IACvC,MAAM,SAAS,GAAG,OAAO,CAAC,GAAG,EAAE,CAAC;IAChC,MAAM,MAAM,GAAG,IAAI,CAAC,QAAQ,CAAC,WAAW,CAAC,CAAC;IAC1C,MAAM,iBAAiB,GAAG,IAAI,CAAC,QAAQ,CAAC,uBAAuB,CAAC,CAAC;IACjE,MAAM,WAAW,GAAG,aAAa,EAAE,CAAC;IAEpC,OAAO,CAAC,GAAG,CAAC,2BAA2B,WAAW,UAAU,CAAC,CAAC;IAC9D,OAAO,CAAC,GAAG,CAAC,aAAa,SAAS,EAAE,CAAC,CAAC;IACtC,IAAI,MAAM;QAAE,OAAO,CAAC,GAAG,CAAC,wCAAwC,CAAC,CAAC;IAClE,OAAO,CAAC,GAAG,CAAC,EAAE,CAAC,CAAC;IAEhB,MAAM,OAAO,GAAoB,EAAE,CAAC;IAEpC,0EAA0E;IAC1E,6EAA6E;IAC7E,2EAA2E;IAC3E,MAAM,QAAQ,GAAG,IAAI,CAAC,IAAI,CAAC,SAAS,EAAE,QAAQ,CAAC,CAAC;IAChD,MAAM,cAAc,GAAG,EAAE,CAAC,UAAU,CAAC,QAAQ,CAAC,CAAC;IAE/C,IAAI,CAAC,cAAc,EAAE,CAAC;QACpB,OAAO,CAAC,GAAG,CACT,yFAAyF,CAC1F,CAAC;QACF,OAAO,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC;IAClB,CAAC;IAED,KAAK,MAAM,EAAE,QAAQ,EAAE,WAAW,EAAE,IAAI,QAAQ,EAAE,CAAC;QACjD,MAAM,aAAa,GAAG,IAAI,CAAC,IAAI,CAAC,QAAQ,EAAE,QAAQ,CAAC,CAAC;QACpD,MAAM,OAAO,GAAG,IAAI,CAAC,IAAI,CAAC,QAAQ,EAAE,OAAO,EAAE,WAAW,CAAC,CAAC;QAE1D,yEAAyE;QACzE,IAAI,CAAC,EAAE,CAAC,UAAU,CAAC,aAAa,CAAC,EAAE,CAAC;YAClC,SAAS;QACX,CAAC;QAED,2EAA2E;QAC3E,IAAI,CAAC,EAAE,CAAC,UAAU,CAAC,OAAO,CAAC,EAAE,CAAC;YAC5B,OAAO,CAAC,IAAI,CAAC,EAAE,IAAI,EAAE,UAAU,QAAQ,EAAE,EAAE,MAAM,EAAE,MAAM,EAAE,CAAC,CAAC;YAC7D,SAAS;QACX,CAAC;QAED,MAAM,WAAW,GAAG,gBAAgB,CAAC,SAAS,EAAE,QAAQ,EAAE,WAAW,EAAE,MAAM,CAAC,CAAC;QAC/E,OAAO,CAAC,IAAI,CAAC,GAAG,WAAW,CAAC,CAAC;IAC/B,CAAC;IAED,wEAAwE;IACxE,2DAA2D;IAC3D,MAAM,aAAa,GAAG,WAAW,CAAC,SAAS,EAAE,WAAW,EAAE,MAAM,EAAE;QAChE,iBAAiB;KAClB,CAAC,CAAC;IACH,OAAO,CAAC,IAAI,CAAC,GAAG,aAAa,CAAC,CAAC;IAE/B,2DAA2D;IAC3D,mEAAmE;IACnE,2EAA2E;IAC3E,MAAM,UAAU,GAAG,cAAc,CAAC,SAAS,EAAE,MAAM,CAAC,CAAC;IACrD,OAAO,CAAC,IAAI,CAAC,GAAG,UAAU,CAAC,CAAC;IAE5B,YAAY,CAAC,OAAO,EAAE,MAAM,CAAC,CAAC;AAChC,CAAC;AAED;;;;GAIG;AACH,SAAS,cAAc,CAAC,SAAiB,EAAE,MAAe;IACxD,MAAM,OAAO,GAAG,IAAI,CAAC,IAAI,CAAC,SAAS,EAAE,WAAW,CAAC,CAAC;IAClD,IAAI,CAAC,EAAE,CAAC,UAAU,CAAC,OAAO,CAAC,EAAE,CAAC;QAC5B,OAAO,EAAE,CAAC;IACZ,CAAC;IAED,IAAI,MAA8E,CAAC;IACnF,IAAI,CAAC;QACH,MAAM,GAAG,IAAI,CAAC,KAAK,CAAC,EAAE,CAAC,YAAY,CAAC,OAAO,EAAE,MAAM,CAAC,CAAkB,CAAC;IACzE,CAAC;IAAC,MAAM,CAAC;QACP,OAAO,CAAC,EAAE,IAAI,EAAE,WAAW,EAAE,MAAM,EAAE,MAAM,EAAE,CAAC,CAAC;IACjD,CAAC;IAED,MAAM,KAAK,GAAG,MAAM,CAAC,UAAU,EAAE,OAAO,CAAC;IACzC,IAAI,CAAC,KAAK;QAAE,OAAO,EAAE,CAAC;IAEtB,6CAA6C;IAC7C,MAAM,KAAK,GACT,KAAK,CAAC,OAAO,KAAK,KAAK;QACvB,KAAK,CAAC,OAAO,CAAC,KAAK,CAAC,IAAI,CAAC;QACzB,KAAK,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,KAAK,SAAS,IAAI,CAAC,KAAK,sBAAsB,CAAC,CAAC;IAE1E,IAAI,CAAC,KAAK;QAAE,OAAO,CAAC,EAAE,IAAI,EAAE,WAAW,EAAE,MAAM,EAAE,SAAS,EAAE,CAAC,CAAC;IAE9D,qCAAqC;IACrC,MAAM,QAAQ,GAAG,IAAI,CAAC,IAAI,CACxB,SAAS,EACT,cAAc,EACd,cAAc,EACd,SAAS,EACT,MAAM,EACN,KAAK,EACL,UAAU,CACX,CAAC;IACF,IAAI,CAAC,EAAE,CAAC,UAAU,CAAC,QAAQ,CAAC,EAAE,CAAC;QAC7B,OAAO,CAAC,EAAE,IAAI,EAAE,WAAW,EAAE,MAAM,EAAE,SAAS,EAAE,CAAC,CAAC;IACpD,CAAC;IAED,8BAA8B;IAC9B,KAAK,CAAC,OAAO,GAAG,MAAM,CAAC;IACvB,KAAK,CAAC,IAAI,GAAG,CAAC,qDAAqD,EAAE,OAAO,CAAC,CAAC;IAE9E,IAAI,CAAC,MAAM,EAAE,CAAC;QACZ,EAAE,CAAC,aAAa,CAAC,OAAO,EAAE,IAAI,CAAC,SAAS,CAAC,MAAM,EAAE,IAAI,EAAE,CAAC,CAAC,GAAG,IAAI,CAAC,CAAC;IACpE,CAAC;IAED,OAAO;QACL;YACE,IAAI,EAAE,wDAAwD;YAC9D,MAAM,EAAE,SAAS;SAClB;KACF,CAAC;AACJ,CAAC;AAED,SAAS,YAAY,CAAC,OAAwB,EAAE,MAAe;IAC7D,OAAO,CAAC,GAAG,CAAC,EAAE,CAAC,CAAC;IAEhB,MAAM,SAAS,GAAG,OAAO,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,MAAM,KAAK,WAAW,CAAC,CAAC;IAClE,MAAM,OAAO,GAAG,OAAO,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,MAAM,KAAK,SAAS,CAAC,CAAC;IAC9D,MAAM,OAAO,GAAG,OAAO,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,MAAM,KAAK,SAAS,CAAC,CAAC;IAC9D,MAAM,MAAM,GAAG,OAAO,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,MAAM,KAAK,MAAM,CAAC,CAAC;IAE1D,IAAI,SAAS,CAAC,MAAM,EAAE,CAAC;QACrB,OAAO,CAAC,GAAG,CAAC,YAAY,CAAC,CAAC;QAC1B,SAAS,CAAC,OAAO,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,OAAO,CAAC,GAAG,CAAC,OAAO,CAAC,CAAC,IAAI,EAAE,CAAC,CAAC,CAAC;IACzD,CAAC;IACD,IAAI,OAAO,CAAC,MAAM,EAAE,CAAC;QACnB,OAAO,CAAC,GAAG,CAAC,UAAU,CAAC,CAAC;QACxB,OAAO,CAAC,OAAO,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,OAAO,CAAC,GAAG,CAAC,OAAO,CAAC,CAAC,IAAI,EAAE,CAAC,CAAC,CAAC;IACvD,CAAC;IACD,IAAI,OAAO,CAAC,MAAM,EAAE,CAAC;QACnB,OAAO,CAAC,GAAG,CAAC,qBAAqB,CAAC,CAAC;QACnC,OAAO,CAAC,OAAO,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,OAAO,CAAC,GAAG,CAAC,OAAO,CAAC,CAAC,IAAI,EAAE,CAAC,CAAC,CAAC;IACvD,CAAC;IACD,IAAI,MAAM,CAAC,MAAM,EAAE,CAAC;QAClB,OAAO,CAAC,GAAG,CAAC,WAAW,CAAC,CAAC;QACzB,MAAM,CAAC,OAAO,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,OAAO,CAAC,GAAG,CAAC,OAAO,CAAC,CAAC,IAAI,EAAE,CAAC,CAAC,CAAC;IACtD,CAAC;IAED,IAAI,CAAC,MAAM,EAAE,CAAC;QACZ,OAAO,CAAC,GAAG,CAAC,4BAA4B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package/dist/cli/index.js

@@ -8,6 +8,7 @@ import { runServe } from './commands/serve.js';
 import { runCache } from './commands/cache.js';
 import { runCatalyze } from './commands/catalyze/index.js';
 import { runUpgrade } from './commands/upgrade.js';
+import { runObsidian } from './commands/obsidian.js';
 const [, , cmd, ...rest] = process.argv;
 if (!cmd || cmd === 'help' || cmd === '--help' || cmd === '-h') {
     printHelp();
@@ -38,6 +39,9 @@ switch (cmd) {
     case 'upgrade':
         runUpgrade(rest);
         break;
+    case 'obsidian':
+        runObsidian(rest);
+        break;
     default:
         console.error(`\nUnknown command: ${cmd}`);
         printHelp();
@@ -60,6 +64,8 @@ Commands:
   serve      Start the MCP server (stdio transport — called by Claude Code via .mcp.json)
   cache      Manage review cache (check, set, clear)
   upgrade    Re-sync installed hooks and update policy.yaml version stamp
+             Options: --dry-run, --clean-blocked-paths
+  obsidian   Sync project state to an Obsidian vault (opt-in)
   help       Show this help
 
 Options for init:
@@ -71,6 +77,8 @@ Options for init:
   --tasks-channel     Discord channel ID for task events
   --releases-channel  Discord channel ID for release events
   --dev-channel       Discord channel ID for dev activity
+  --obsidian          Configure Obsidian vault integration in gateway.yaml
+  --vault-path <path> Obsidian vault path (used with --obsidian)
 
 Options for catalyze [targetDir]:
   --plan              Analyze stack and generate report (default)
@@ -104,6 +112,7 @@ Examples:
   npx @bookedsolid/reagent serve
   npx @bookedsolid/reagent upgrade
   npx @bookedsolid/reagent upgrade --dry-run
+  npx @bookedsolid/reagent upgrade --clean-blocked-paths
 `);
 }
 //# sourceMappingURL=index.js.map

package/dist/cli/index.js.map

@@ -1 +1 @@
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+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/cli/index.ts"],"names":[],"mappings":";AAEA,OAAO,EAAE,aAAa,EAAE,MAAM,YAAY,CAAC;AAC3C,OAAO,EAAE,OAAO,EAAE,MAAM,0BAA0B,CAAC;AACnD,OAAO,EAAE,QAAQ,EAAE,MAAM,qBAAqB,CAAC;AAC/C,OAAO,EAAE,SAAS,EAAE,MAAM,sBAAsB,CAAC;AACjD,OAAO,EAAE,WAAW,EAAE,MAAM,wBAAwB,CAAC;AACrD,OAAO,EAAE,QAAQ,EAAE,MAAM,qBAAqB,CAAC;AAC/C,OAAO,EAAE,QAAQ,EAAE,MAAM,qBAAqB,CAAC;AAC/C,OAAO,EAAE,WAAW,EAAE,MAAM,8BAA8B,CAAC;AAC3D,OAAO,EAAE,UAAU,EAAE,MAAM,uBAAuB,CAAC;AACnD,OAAO,EAAE,WAAW,EAAE,MAAM,wBAAwB,CAAC;AAErD,MAAM,CAAC,EAAE,AAAD,EAAG,GAAG,EAAE,GAAG,IAAI,CAAC,GAAG,OAAO,CAAC,IAAI,CAAC;AAExC,IAAI,CAAC,GAAG,IAAI,GAAG,KAAK,MAAM,IAAI,GAAG,KAAK,QAAQ,IAAI,GAAG,KAAK,IAAI,EAAE,CAAC;IAC/D,SAAS,EAAE,CAAC;IACZ,OAAO,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC;AAClB,CAAC;AAED,QAAQ,GAAG,EAAE,CAAC;IACZ,KAAK,MAAM;QACT,OAAO,CAAC,IAAI,CAAC,CAAC;QACd,MAAM;IACR,KAAK,OAAO;QACV,QAAQ,CAAC,IAAI,CAAC,CAAC;QACf,MAAM;IACR,KAAK,QAAQ;QACX,SAAS,CAAC,IAAI,CAAC,CAAC;QAChB,MAAM;IACR,KAAK,UAAU;QACb,WAAW,CAAC,IAAI,CAAC,CAAC;QAClB,MAAM;IACR,KAAK,OAAO;QACV,MAAM,QAAQ,CAAC,IAAI,CAAC,CAAC;QACrB,MAAM;IACR,KAAK,OAAO;QACV,QAAQ,CAAC,IAAI,CAAC,CAAC;QACf,MAAM;IACR,KAAK,UAAU;QACb,WAAW,CAAC,IAAI,CAAC,CAAC;QAClB,MAAM;IACR,KAAK,SAAS;QACZ,UAAU,CAAC,IAAI,CAAC,CAAC;QACjB,MAAM;IACR,KAAK,UAAU;QACb,WAAW,CAAC,IAAI,CAAC,CAAC;QAClB,MAAM;IACR;QACE,OAAO,CAAC,KAAK,CAAC,sBAAsB,GAAG,EAAE,CAAC,CAAC;QAC3C,SAAS,EAAE,CAAC;QACZ,OAAO,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC;AACpB,CAAC;AAED,SAAS,SAAS;IAChB,MAAM,WAAW,GAAG,aAAa,EAAE,CAAC;IACpC,OAAO,CAAC,GAAG,CAAC;wBACU,WAAW;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;CA+DlC,CAAC,CAAC;AACH,CAAC"}

package/dist/gateway/native-tools.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"native-tools.d.ts","sourceRoot":"","sources":["../../src/gateway/native-tools.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,SAAS,EAAE,MAAM,yCAAyC,CAAC;AAKzE,OAAO,KAAK,EAAE,UAAU,EAAqB,MAAM,uBAAuB,CAAC;AAI3E;;;GAGG;AACH,wBAAgB,mBAAmB,CACjC,OAAO,EAAE,SAAS,EAClB,OAAO,EAAE,MAAM,EACf,WAAW,EAAE,UAAU,EAAE,GACxB,MAAM,CAyTR"}
+{"version":3,"file":"native-tools.d.ts","sourceRoot":"","sources":["../../src/gateway/native-tools.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,SAAS,EAAE,MAAM,yCAAyC,CAAC;AAMzE,OAAO,KAAK,EAAE,UAAU,EAAqB,MAAM,uBAAuB,CAAC;AAI3E;;;GAGG;AACH,wBAAgB,mBAAmB,CACjC,OAAO,EAAE,SAAS,EAClB,OAAO,EAAE,MAAM,EACf,WAAW,EAAE,UAAU,EAAE,GACxB,MAAM,CAyWR"}

package/dist/gateway/native-tools.js

@@ -2,6 +2,7 @@ import { z } from 'zod';
 import { TaskStore } from '../pm/task-store.js';
 import { GitHubBridge } from '../pm/github-bridge.js';
 import { DiscordNotifier } from '../pm/discord-notifier.js';
+import { VaultWriter } from '../obsidian/vault-writer.js';
 import { executeChain } from './middleware/chain.js';
 import { InvocationStatus } from '../types/index.js';
 /**
@@ -12,6 +13,7 @@ export function registerNativeTools(gateway, baseDir, middlewares) {
     const store = new TaskStore(baseDir);
     const bridge = new GitHubBridge({ baseDir });
     const discord = new DiscordNotifier(baseDir);
+    const obsidian = new VaultWriter(baseDir);
     let count = 0;
     function wrapHandler(toolName, handler) {
         return async (params) => {
@@ -247,6 +249,43 @@ export function registerNativeTools(gateway, baseDir, middlewares) {
         return { sent: true, channel, note: 'Notification dispatched (best-effort)' };
     }));
     count++;
+    // ── obsidian_sync ─────────────────────────────────────────────────
+    gateway.tool('obsidian_sync', 'Sync project state to an Obsidian vault. Requires obsidian_vault to be enabled in .reagent/gateway.yaml and REAGENT_OBSIDIAN_VAULT env var (or vault_path in config).', {
+        target: z
+            .enum(['kanban', 'context', 'wiki', 'tasks', 'all'])
+            .optional()
+            .default('all')
+            .describe('Sync target (default: all enabled targets)'),
+        dry_run: z
+            .boolean()
+            .optional()
+            .default(false)
+            .describe('Preview what would be written without writing files'),
+    }, wrapHandler('obsidian_sync', (args) => {
+        if (!obsidian.isEnabled()) {
+            return {
+                error: 'Obsidian vault integration is not enabled. Set obsidian_vault.enabled: true in .reagent/gateway.yaml and set REAGENT_OBSIDIAN_VAULT env var.',
+            };
+        }
+        const target = args.target || 'all';
+        const dryRun = args.dry_run || false;
+        if (target === 'all') {
+            return obsidian.syncAll(dryRun);
+        }
+        switch (target) {
+            case 'kanban':
+                return obsidian.syncKanban(dryRun);
+            case 'context':
+                return obsidian.syncContextDump(dryRun);
+            case 'wiki':
+                return obsidian.syncWiki(dryRun);
+            case 'tasks':
+                return obsidian.syncTasks(dryRun);
+            default:
+                return { error: `Unknown target: ${target}` };
+        }
+    }));
+    count++;
     console.error(`[reagent] Registered ${count} native tools`);
     return count;
 }