cortex-engine 0.4.2 → 0.5.1

package/dist/bin/init.js

@@ -199,13 +199,30 @@ const MCP_JSON = `{
   }
 }
 `;
-const COGNITIVE_TOOLS_REFERENCE = `# Cognitive Tools
+// ─── TOOLS.md — Agent-Agnostic Tool Reference ────────────────────────────
+// This is the canonical reference. Lives at .fozikio/TOOLS.md.
+// Any agent on any platform reads this file.
+const TOOLS_REFERENCE = `# Cortex Tools
 
-This workspace uses cortex-engine for persistent memory.
+This workspace uses cortex-engine for persistent memory. These tools are available via MCP — any compatible client can use them.
 
-## Tools
+## Use the Right Tool
 
-Read before you write. Tool descriptions tell you the rest.
+Don't dump everything into \`observe()\`. Match the tool to what you're recording:
+
+| What you're recording | Use this | Not this |
+|----------------------|----------|----------|
+| A fact you learned or confirmed | \`observe\` | — |
+| An open question or curiosity | \`wonder\` | observe() |
+| A hypothesis or untested idea | \`speculate\` | observe() |
+| A position that could change with new evidence | \`believe\` | observe() |
+| Something worth deeper processing | \`reflect\` | observe() |
+| Ongoing work or open questions across sessions | \`thread_create\` / \`thread_update\` | observe() |
+| Session reflection at end of day | \`journal_write\` | observe() |
+| Operational breadcrumbs during work | \`ops_append\` | observe() |
+| An identity or behavior change | \`evolve\` | observe() |
+
+## Core Tools (25)
 
 **Write — record knowledge:**
 | Tool | Purpose |
@@ -227,6 +244,14 @@ Read before you write. Tool descriptions tell you the rest.
 | \`neighbors\` | Explore memories connected to a specific concept |
 | \`wander\` | Random walk for serendipitous discovery |
 
+**Threads — ongoing work:**
+| Tool | Purpose |
+|------|---------|
+| \`thread_create\` | Start tracking an ongoing question, project, or exploration |
+| \`thread_update\` | Add progress, change status, link related memories |
+| \`thread_resolve\` | Close a thread with a resolution |
+| \`threads_list\` | See open threads (check at session start) |
+
 **Ops — session tracking:**
 | Tool | Purpose |
 |------|---------|
@@ -234,12 +259,79 @@ Read before you write. Tool descriptions tell you the rest.
 | \`ops_query\` | Search the operational log |
 | \`ops_update\` | Update an ops entry status or content |
 
+**Identity:**
+| Tool | Purpose |
+|------|---------|
+| \`evolve\` | Propose a change to values, preferences, or patterns |
+| \`evolution_list\` | View pending or applied identity proposals |
+| \`journal_write\` | Write a daily reflective entry |
+| \`journal_read\` | Read past journal entries |
+
 **System:**
 | Tool | Purpose |
 |------|---------|
 | \`stats\` | Memory counts and namespace health |
 | \`dream\` | Consolidate observations into long-term memories (run periodically) |
+
+## Hard Rules
+
+1. **Read before you write** — call \`query()\` before adding to cortex. Check what you already know.
+2. **Use the full tool suite** — if you're only using observe/query, you're missing the point. Threads, journals, beliefs, and reflections exist for a reason.
+3. **Check threads at session start** — call \`threads_list()\` to see what's in progress before starting new work.
+`;
+// ─── CLAUDE.md — Claude Code Platform Pointer ────────────────────────────
+// Thin pointer to TOOLS.md + Claude-specific context (hooks, skills).
+const CLAUDE_MD = `# Cognitive Tools
+
+This workspace uses [cortex-engine](https://github.com/Fozikio/cortex-engine) for persistent memory.
+
+**Read \`.fozikio/TOOLS.md\` for the full tool reference** — all 25+ cognitive tools with usage guidance.
+
+## Quick Reference
+
+- Before substantive work → \`query()\` to ground in accumulated knowledge
+- Facts → \`observe()\` | Questions → \`wonder()\` | Positions → \`believe()\`
+- Ongoing work → \`thread_create()\` / \`thread_update()\`
+- Session end → \`journal_write()\`
+- Operational logs → \`ops_append()\`
+
+## Installed Hooks
+
+Hooks in \`.claude/hooks/\` fire automatically on Claude Code events. Read the comment headers in each \`.sh\` file for details.
+
+## Installed Skills
+
+Skills in \`.claude/skills/\` are invocable workflows. Use \`/skill-name\` to run them.
+
+## Safety Rules
+
+Reflex rules in \`reflex-rules/\` enforce cognitive habits. See [@fozikio/reflex](https://github.com/Fozikio/reflex) for format details.
 `;
+// ─── AGENTS.md — Multi-Agent Roster ──────────────────────────────────────
+// NOT a tool reference. Lists who's in the workspace and what they do.
+function buildAgentsRoster(name) {
+    return [
+        '# Agents',
+        '',
+        `## ${name}`,
+        '',
+        'This workspace has a single agent. The agent\'s identity is defined in `.fozikio/mind/profile.md`.',
+        '',
+        '### Cognitive Tools',
+        '',
+        'See `.fozikio/TOOLS.md` for the full tool reference.',
+        '',
+        '### Adding More Agents',
+        '',
+        '```bash',
+        'npx fozikio agent add researcher --description "Research agent"',
+        'npx fozikio agent generate-mcp',
+        '```',
+        '',
+        'Each agent gets its own namespace with isolated memory. See [multi-agent docs](https://github.com/Fozikio/cortex-engine/blob/master/docs/multi-agent-design.md) for details.',
+        '',
+    ].join('\n');
+}
 const OBSIDIAN_APP_JSON = `{
   "legacyEditor": false,
   "livePreview": true,
@@ -251,6 +343,61 @@ const OBSIDIAN_APPEARANCE_JSON = `{
   "theme": "obsidian"
 }
 `;
+// ─── Plugin Detection ─────────────────────────────────────────────────────
+/** Plugin metadata for TOOLS.md generation */
+const KNOWN_PLUGINS = {
+    '@fozikio/tools-content': {
+        description: 'Content pipeline — draft, review, publish workflow',
+        tools: '`content_create`, `content_list`, `content_update`',
+    },
+    '@fozikio/tools-social': {
+        description: 'Social cognition — interaction patterns, engagement tracking',
+        tools: '`social_read`, `social_update`',
+    },
+    '@fozikio/tools-graph': {
+        description: 'Graph analysis — memory connections, clustering, visualization',
+        tools: '`graph_report`, `suggest_links`, `find_duplicates`',
+    },
+    '@fozikio/tools-maintenance': {
+        description: 'Memory maintenance — cleanup, deduplication, health checks',
+        tools: '`consolidation_status`, `sleep_pressure`',
+    },
+    '@fozikio/tools-vitals': {
+        description: 'Vitals tracking — agent health metrics and operational signals',
+        tools: '`vitals_get`, `vitals_set`',
+    },
+    '@fozikio/tools-reasoning': {
+        description: 'Cognitive reasoning — abstraction, contradiction, surfacing',
+        tools: '`abstract`, `contradict`, `surface`, `notice`, `resolve`, `intention`, `predict`',
+    },
+};
+/**
+ * Scan for installed @fozikio/tools-* plugin packages and return
+ * a markdown section listing their tools for TOOLS.md.
+ */
+function detectInstalledPlugins(targetDir) {
+    const found = [];
+    for (const [pkg, meta] of Object.entries(KNOWN_PLUGINS)) {
+        try {
+            const pkgJsonPath = join(targetDir, 'node_modules', ...pkg.split('/'), 'package.json');
+            if (existsSync(pkgJsonPath)) {
+                found.push({ name: pkg, ...meta });
+            }
+        }
+        catch {
+            // skip
+        }
+    }
+    if (found.length === 0)
+        return null;
+    let section = '\n## Installed Plugins\n\n';
+    for (const plugin of found) {
+        section += `**${plugin.name}** — ${plugin.description}\n`;
+        section += `Tools: ${plugin.tools}\n\n`;
+    }
+    section += `*Plugins are auto-detected from node_modules. Install more with \`npm install @fozikio/tools-<name>\`.*\n`;
+    return section;
+}
 // ─── Manifest & Asset Installation ────────────────────────────────────────
 /** Resolve the package root (where fozikio.json lives). */
 function getPackageRoot() {
@@ -300,6 +447,28 @@ function installHooks(packageRoot, targetDir, hooks) {
     }
     return installed;
 }
+function installReflexRules(packageRoot, targetDir, rules) {
+    const sourceDir = join(packageRoot, 'reflex-rules');
+    const destDir = join(targetDir, 'reflex-rules');
+    const installed = [];
+    if (!existsSync(sourceDir)) {
+        console.error('[fozikio] Warning: reflex-rules/ directory not found in package — skipping rule installation.');
+        return installed;
+    }
+    mkdirSync(destDir, { recursive: true });
+    for (const rule of rules) {
+        const ruleFile = `${rule}.yaml`;
+        const src = join(sourceDir, ruleFile);
+        if (!existsSync(src)) {
+            console.error(`[fozikio] Warning: reflex rule not found: ${ruleFile} — skipping.`);
+            continue;
+        }
+        const dest = join(destDir, ruleFile);
+        cpSync(src, dest);
+        installed.push(ruleFile);
+    }
+    return installed;
+}
 function installSkills(packageRoot, targetDir, skills) {
     const sourceDir = join(packageRoot, 'skills');
     const destDir = join(targetDir, '.claude', 'skills');
@@ -370,10 +539,18 @@ export function runInit(args) {
     writeFileSync(join(credentialsDir, '.gitignore'), '*\n!.gitignore\n', 'utf-8');
     // .mcp.json
     writeFileSync(join(targetDir, '.mcp.json'), MCP_JSON, 'utf-8');
-    // CLAUDE.md
-    writeFileSync(join(targetDir, 'CLAUDE.md'), COGNITIVE_TOOLS_REFERENCE, 'utf-8');
-    // AGENTS.md
-    writeFileSync(join(targetDir, 'AGENTS.md'), COGNITIVE_TOOLS_REFERENCE, 'utf-8');
+    // .fozikio/TOOLS.md — canonical agent-agnostic tool reference
+    let toolsContent = TOOLS_REFERENCE;
+    // Detect installed plugins and append their tool sections
+    const pluginSections = detectInstalledPlugins(targetDir);
+    if (pluginSections) {
+        toolsContent += pluginSections;
+    }
+    writeFileSync(join(fozikioDir, 'TOOLS.md'), toolsContent, 'utf-8');
+    // CLAUDE.md — thin pointer for Claude Code users
+    writeFileSync(join(targetDir, 'CLAUDE.md'), CLAUDE_MD, 'utf-8');
+    // AGENTS.md — multi-agent roster
+    writeFileSync(join(targetDir, 'AGENTS.md'), buildAgentsRoster(opts.name), 'utf-8');
     // .obsidian/
     if (opts.obsidian) {
         const obsidianDir = join(targetDir, '.obsidian');
@@ -386,7 +563,7 @@ export function runInit(args) {
     const manifest = loadManifest(packageRoot);
     const installedHooks = [];
     const installedSkills = [];
-    let hasReflexRules = false;
+    const installedRules = [];
     if (manifest?.contents) {
         if (manifest.contents.hooks && manifest.contents.hooks.length > 0) {
             installedHooks.push(...installHooks(packageRoot, targetDir, manifest.contents.hooks));
@@ -394,7 +571,10 @@ export function runInit(args) {
         if (manifest.contents.skills && manifest.contents.skills.length > 0) {
             installedSkills.push(...installSkills(packageRoot, targetDir, manifest.contents.skills));
         }
-        hasReflexRules = (manifest.contents.reflex_rules ?? manifest.contents.hookify_rules ?? []).length > 0;
+        const reflexRuleNames = manifest.contents.reflex_rules ?? manifest.contents.hookify_rules ?? [];
+        if (reflexRuleNames.length > 0) {
+            installedRules.push(...installReflexRules(packageRoot, targetDir, reflexRuleNames));
+        }
     }
     // Success message
     const relativePath = opts.here ? '.' : opts.name;
@@ -409,6 +589,7 @@ export function runInit(args) {
     console.error(`  ${relativePath}/.fozikio/journal/`);
     console.error(`  ${relativePath}/.fozikio/state/templates/`);
     console.error(`  ${relativePath}/.fozikio/credentials/.gitignore`);
+    console.error(`  ${relativePath}/.fozikio/TOOLS.md`);
     console.error(`  ${relativePath}/.mcp.json`);
     console.error(`  ${relativePath}/CLAUDE.md`);
     console.error(`  ${relativePath}/AGENTS.md`);
@@ -430,10 +611,13 @@ export function runInit(args) {
             console.error(`  ${relativePath}/.claude/skills/${skill}/`);
         }
     }
-    if (hasReflexRules) {
+    if (installedRules.length > 0) {
         console.error('');
-        console.error('Reflex safety rules available. Run `fozikio install-rules` to install.');
-        console.error('  See: https://github.com/Fozikio/reflex');
+        console.error('Reflex safety rules installed:');
+        for (const rule of installedRules) {
+            console.error(`  ${relativePath}/reflex-rules/${rule}`);
+        }
+        console.error('  Validate with: npx reflex validate reflex-rules');
     }
     console.error('');
     console.error('Next steps:');

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package/dist/bin/maintain-cmd.d.ts

@@ -0,0 +1,17 @@
+/**
+ * maintain-cmd.ts — fozikio maintain command.
+ *
+ * Subcommands:
+ *   fozikio maintain fix              Scan and repair data issues
+ *   fozikio maintain re-embed         Re-embed all memories with current provider
+ *   fozikio maintain re-embed --dry-run  Show what would be re-embedded
+ *
+ * Flags:
+ *   --dry-run     Show what would change without writing
+ *   --limit N     Max memories to process (default: 500)
+ *   --collection  memories | observations (for re-embed, default: memories)
+ *   --null-only   Re-embed only docs with null/empty embeddings
+ *   --verbose     Detailed per-item output
+ */
+export declare function runMaintain(args: string[]): Promise<void>;
+//# sourceMappingURL=maintain-cmd.d.ts.map

package/dist/bin/maintain-cmd.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"maintain-cmd.d.ts","sourceRoot":"","sources":["../../src/bin/maintain-cmd.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;GAcG;AAyXH,wBAAsB,WAAW,CAAC,IAAI,EAAE,MAAM,EAAE,GAAG,OAAO,CAAC,IAAI,CAAC,CAuB/D"}