cortex-engine 0.1.0 → 0.2.0

package/dist/bin/init.js

@@ -1,11 +1,11 @@
 /**
- * init.ts — cortex-kit init command.
+ * init.ts — fozikio init command.
  *
  * Scaffolds a new agent workspace with cortex-engine configuration.
  *
  * Usage:
- *   cortex-kit init <name> [options]
- *   cortex-kit init --here [options]
+ *   fozikio init <name> [options]
+ *   fozikio init --here [options]
  *
  * Options:
  *   --store sqlite|firestore   Storage backend (default: sqlite)
@@ -41,7 +41,7 @@ export function parseInitArgs(args) {
         else if (arg === '--store') {
             const val = args[++i];
             if (val !== 'sqlite' && val !== 'firestore') {
-                console.error(`[cortex-kit] Invalid --store value: ${val}. Must be sqlite or firestore.`);
+                console.error(`[fozikio] Invalid --store value: ${val}. Must be sqlite or firestore.`);
                 return null;
             }
             opts.store = val;
@@ -49,7 +49,7 @@ export function parseInitArgs(args) {
         else if (arg === '--embed') {
             const val = args[++i];
             if (val !== 'ollama' && val !== 'vertex' && val !== 'openai') {
-                console.error(`[cortex-kit] Invalid --embed value: ${val}. Must be ollama, vertex, or openai.`);
+                console.error(`[fozikio] Invalid --embed value: ${val}. Must be ollama, vertex, or openai.`);
                 return null;
             }
             opts.embed = val;
@@ -57,7 +57,7 @@ export function parseInitArgs(args) {
         else if (arg === '--llm') {
             const val = args[++i];
             if (val !== 'ollama' && val !== 'gemini' && val !== 'anthropic' && val !== 'openai') {
-                console.error(`[cortex-kit] Invalid --llm value: ${val}. Must be ollama, gemini, anthropic, or openai.`);
+                console.error(`[fozikio] Invalid --llm value: ${val}. Must be ollama, gemini, anthropic, or openai.`);
                 return null;
             }
             opts.llm = val;
@@ -69,15 +69,15 @@ export function parseInitArgs(args) {
             opts.name = arg;
         }
         else {
-            console.error(`[cortex-kit] Unknown option: ${arg}`);
+            console.error(`[fozikio] Unknown option: ${arg}`);
             return null;
         }
         i++;
     }
     if (!opts.here && !opts.name) {
-        console.error('[cortex-kit] init requires a name argument or --here flag.');
-        console.error('  Usage: cortex-kit init <name>');
-        console.error('         cortex-kit init --here');
+        console.error('[fozikio] init requires a name argument or --here flag.');
+        console.error('  Usage: fozikio init <name>');
+        console.error('         fozikio init --here');
         return null;
     }
     // When --here, derive name from current directory
@@ -87,97 +87,156 @@ export function parseInitArgs(args) {
     return opts;
 }
 // ─── Templates ─────────────────────────────────────────────────────────────
-function buildConfigYaml(opts) {
-    return `agent:
+function buildAgentYaml(opts) {
+    return `# Fozikio Agent — Identity & Connection Manifest
+
+agent:
   name: ${opts.name}
-  type: general
+  version: "1.0"
+
+identity:
+  profile: mind/profile.md
+  session_state: state/session-state.md
 
 cortex:
-  store: ${opts.store}
-  embed: ${opts.embed}
-  llm: ${opts.llm}
+  ${opts.namespace}:
+    store: ${opts.store}
+    embed: ${opts.embed}
+    primary: true
 
-  namespaces:
-    ${opts.namespace}:
-      default: true
-      description: "Default namespace"
-      cognitive_tools:
-        - observe
-        - query
-        - recall
-        - neighbors
-        - predict
-        - reflect
-        - dream
-      collections_prefix: ""
+credentials:
+  dir: credentials/
+  encryption: none
 `;
 }
-const MCP_JSON = `{
-  "mcpServers": {
-    "cortex": {
-      "command": "npx",
-      "args": ["cortex-engine"]
-    }
-  }
+function buildAgentKitJson() {
+    return `{
+  "version": "1.0",
+  "hooks": [],
+  "skills": [],
+  "agents": []
 }
 `;
-const COGNITIVE_TOOLS_REFERENCE = `# Cognitive Tools
+}
+function buildFozikioReadme(name) {
+    return `# .fozikio/
 
-This workspace uses cortex-engine for persistent memory and cognition.
+This directory is the agent workspace manifest for **${name}**.
 
-## Available Tools
+It is read by cortex-engine and fozikio to configure the agent's identity,
+storage backend, embedding provider, and installed components.
 
-| Tool | What it does |
-|------|-------------|
-| \`observe\` | Record an observation — cortex decides if it's novel, similar, or duplicate |
-| \`query\` | Semantic search across memory with HyDE expansion |
-| \`recall\` | Browse recent observations and memories by time |
-| \`neighbors\` | Explore the memory graph from a specific concept |
-| \`predict\` | Proactive retrieval — what's relevant given current context |
-| \`validate\` | Check a prediction against an outcome (FSRS learning) |
-| \`believe\` | Record a belief change with reason tracking |
-| \`reflect\` | Generate reflective insights connecting observations |
-| \`dream\` | Run consolidation — cluster, refine, create, connect, score, abstract |
-| \`digest\` | Process a document through the ingestion pipeline |
-| \`stats\` | Memory counts and namespace health |
-| \`ops_append\` | Log operational breadcrumbs |
-| \`ops_query\` | Query the operational log |
-| \`ops_update\` | Update an ops entry |
-| \`wander\` | Random graph walk for serendipitous discovery |
+## Files
 
-## Usage Pattern
+| File | Purpose |
+|------|---------|
+| \`agent.yaml\` | Identity manifest — agent name, cortex config, credentials |
+| \`agent-kit.json\` | Installable components — hooks, skills, agents |
+| \`mind/profile.md\` | Agent identity profile (who this agent is) |
+| \`knowledge/_index.md\` | Knowledge base index |
+| \`journal/\` | Session journal entries |
+| \`state/templates/\` | Note templates for structured memory |
+| \`credentials/\` | Local credentials (gitignored) |
 
-Before working on any topic, query cortex first:
-\`\`\`
-query("the topic you're working on")
-\`\`\`
+## Usage
 
-When you learn something interesting:
+Start the MCP server:
 \`\`\`
-observe("what you noticed")
+npx cortex-engine
 \`\`\`
 
-At session end, run dream to consolidate:
-\`\`\`
-dream()
-\`\`\`
+Or configure via .mcp.json and let your MCP client manage the lifecycle.
+`;
+}
+function buildMindProfile(name) {
+    return `---
+type: mind
+status: active
+tags: []
+---
+
+# ${name}
+
+## Identity
+
+*Who is this agent? Fill in your identity here.*
+
+## Values
+
+-
 
-## Installed Hooks
+## Working Style
 
-Cortex-kit hooks are installed in \`.claude/hooks/\`. They fire automatically:
+-
 
-- **cognitive-grounding** — reminds you to \`query()\` before evaluation/design/review work
-- **observe-first** — warns before writing to memory directories without \`observe()\`/\`query()\`
-- **cortex-telemetry** — tracks retrieval patterns for quality feedback
-- **session-lifecycle** — resets session state on startup
-- **project-board-gate** — gates \`git push\` on board updates (configure via \`.claude/state/project-boards.json\`)
+## Goals
 
-To disable any hook, delete its \`.sh\` file from \`.claude/hooks/\`.
+-
 
-## Installed Skills
+## Relationships
 
-- **/cortex-query** — best practices for querying cortex memory
-- **/cortex-review** — structured review workflow grounded in cortex context
+*Key people, systems, and projects this agent interacts with.*
+`;
+}
+const KNOWLEDGE_INDEX = `---
+type: knowledge
+status: active
+tags: []
+---
+
+# Knowledge Index
+
+*Reference material, decisions, and patterns.*
+`;
+const MCP_JSON = `{
+  "mcpServers": {
+    "cortex": {
+      "command": "npx",
+      "args": ["cortex-engine"]
+    }
+  }
+}
+`;
+const COGNITIVE_TOOLS_REFERENCE = `# Cognitive Tools
+
+This workspace uses cortex-engine for persistent memory.
+
+## Tools
+
+Read before you write. Tool descriptions tell you the rest.
+
+**Write — record knowledge:**
+| Tool | Purpose |
+|------|---------|
+| \`observe\` | Record a fact — something you learned, confirmed, or noticed to be true |
+| \`wonder\` | Record an open question or curiosity — stored separately from facts |
+| \`speculate\` | Record a hypothesis or untested idea — excluded from default retrieval |
+| \`believe\` | Update what you believe about an existing memory |
+| \`reflect\` | Synthesize what you know about a topic into a grounded reflection |
+| \`digest\` | Ingest a document — extracts facts and generates reflections |
+
+**Read — retrieve knowledge:**
+| Tool | Purpose |
+|------|---------|
+| \`query\` | Search memories by meaning |
+| \`recall\` | List recent observations chronologically |
+| \`predict\` | Anticipate what memories might be relevant next |
+| \`validate\` | Confirm or deny a prediction — strengthens or weakens the memory |
+| \`neighbors\` | Explore memories connected to a specific concept |
+| \`wander\` | Random walk for serendipitous discovery |
+
+**Ops — session tracking:**
+| Tool | Purpose |
+|------|---------|
+| \`ops_append\` | Log a session breadcrumb, milestone, or decision |
+| \`ops_query\` | Search the operational log |
+| \`ops_update\` | Update an ops entry status or content |
+
+**System:**
+| Tool | Purpose |
+|------|---------|
+| \`stats\` | Memory counts and namespace health |
+| \`dream\` | Consolidate observations into long-term memories (run periodically) |
 `;
 const OBSIDIAN_APP_JSON = `{
   "legacyEditor": false,
@@ -191,16 +250,16 @@ const OBSIDIAN_APPEARANCE_JSON = `{
 }
 `;
 // ─── Manifest & Asset Installation ────────────────────────────────────────
-/** Resolve the package root (where cortex-kit.json lives). */
+/** Resolve the package root (where fozikio.json lives). */
 function getPackageRoot() {
     const thisFile = fileURLToPath(import.meta.url);
     // dist/bin/init.js → package root (two levels up)
     return resolve(dirname(thisFile), '..', '..');
 }
 function loadManifest(packageRoot) {
-    const manifestPath = join(packageRoot, 'cortex-kit.json');
+    const manifestPath = join(packageRoot, 'fozikio.json');
     if (!existsSync(manifestPath)) {
-        console.error('[cortex-kit] Warning: cortex-kit.json not found — skipping hook/skill installation.');
+        console.error('[fozikio] Warning: fozikio.json not found — skipping hook/skill installation.');
         return null;
     }
     try {
@@ -208,7 +267,7 @@ function loadManifest(packageRoot) {
     }
     catch (err) {
         const msg = err instanceof Error ? err.message : String(err);
-        console.error(`[cortex-kit] Warning: Failed to parse cortex-kit.json: ${msg} — skipping hook/skill installation.`);
+        console.error(`[fozikio] Warning: Failed to parse fozikio.json: ${msg} — skipping hook/skill installation.`);
         return null;
     }
 }
@@ -217,7 +276,7 @@ function installHooks(packageRoot, targetDir, hooks) {
     const destDir = join(targetDir, '.claude', 'hooks');
     const installed = [];
     if (!existsSync(sourceDir)) {
-        console.error('[cortex-kit] Warning: hooks/ directory not found in package — skipping hook installation.');
+        console.error('[fozikio] Warning: hooks/ directory not found in package — skipping hook installation.');
         return installed;
     }
     mkdirSync(destDir, { recursive: true });
@@ -225,7 +284,7 @@ function installHooks(packageRoot, targetDir, hooks) {
         const hookFile = `${hook}.sh`;
         const src = join(sourceDir, hookFile);
         if (!existsSync(src)) {
-            console.error(`[cortex-kit] Warning: hook not found: ${hookFile} — skipping.`);
+            console.error(`[fozikio] Warning: hook not found: ${hookFile} — skipping.`);
             continue;
         }
         const dest = join(destDir, hookFile);
@@ -244,14 +303,14 @@ function installSkills(packageRoot, targetDir, skills) {
     const destDir = join(targetDir, '.claude', 'skills');
     const installed = [];
     if (!existsSync(sourceDir)) {
-        console.error('[cortex-kit] Warning: skills/ directory not found in package — skipping skill installation.');
+        console.error('[fozikio] Warning: skills/ directory not found in package — skipping skill installation.');
         return installed;
     }
     mkdirSync(destDir, { recursive: true });
     for (const skill of skills) {
         const src = join(sourceDir, skill);
         if (!existsSync(src)) {
-            console.error(`[cortex-kit] Warning: skill not found: ${skill}/ — skipping.`);
+            console.error(`[fozikio] Warning: skill not found: ${skill}/ — skipping.`);
             continue;
         }
         const dest = join(destDir, skill);
@@ -274,16 +333,39 @@ export function runInit(args) {
         ? process.cwd()
         : resolve(process.cwd(), opts.name);
     if (!opts.here && existsSync(targetDir)) {
-        console.error(`[cortex-kit] Directory already exists: ${targetDir}`);
+        console.error(`[fozikio] Directory already exists: ${targetDir}`);
         console.error('  Use --here to scaffold into the current directory.');
         process.exit(1);
     }
     // Create target directory
     mkdirSync(targetDir, { recursive: true });
-    // .fozikio/config.yaml
+    // .fozikio/ — agent manifest directory
     const fozikioDir = join(targetDir, '.fozikio');
     mkdirSync(fozikioDir, { recursive: true });
-    writeFileSync(join(fozikioDir, 'config.yaml'), buildConfigYaml(opts), 'utf-8');
+    // .fozikio/agent.yaml
+    writeFileSync(join(fozikioDir, 'agent.yaml'), buildAgentYaml(opts), 'utf-8');
+    // .fozikio/agent-kit.json
+    writeFileSync(join(fozikioDir, 'agent-kit.json'), buildAgentKitJson(), 'utf-8');
+    // .fozikio/README.md
+    writeFileSync(join(fozikioDir, 'README.md'), buildFozikioReadme(opts.name), 'utf-8');
+    // .fozikio/mind/profile.md
+    const mindDir = join(fozikioDir, 'mind');
+    mkdirSync(mindDir, { recursive: true });
+    writeFileSync(join(mindDir, 'profile.md'), buildMindProfile(opts.name), 'utf-8');
+    // .fozikio/knowledge/_index.md
+    const knowledgeDir = join(fozikioDir, 'knowledge');
+    mkdirSync(knowledgeDir, { recursive: true });
+    writeFileSync(join(knowledgeDir, '_index.md'), KNOWLEDGE_INDEX, 'utf-8');
+    // .fozikio/journal/ (empty dir — needs a placeholder so it exists in git)
+    const journalDir = join(fozikioDir, 'journal');
+    mkdirSync(journalDir, { recursive: true });
+    // .fozikio/state/templates/ (empty dir)
+    const stateTemplatesDir = join(fozikioDir, 'state', 'templates');
+    mkdirSync(stateTemplatesDir, { recursive: true });
+    // .fozikio/credentials/.gitignore
+    const credentialsDir = join(fozikioDir, 'credentials');
+    mkdirSync(credentialsDir, { recursive: true });
+    writeFileSync(join(credentialsDir, '.gitignore'), '*\n!.gitignore\n', 'utf-8');
     // .mcp.json
     writeFileSync(join(targetDir, '.mcp.json'), MCP_JSON, 'utf-8');
     // CLAUDE.md
@@ -314,10 +396,17 @@ export function runInit(args) {
     }
     // Success message
     const relativePath = opts.here ? '.' : opts.name;
-    console.error(`[cortex-kit] Workspace scaffolded at: ${targetDir}`);
+    console.error(`[fozikio] Workspace scaffolded at: ${targetDir}`);
     console.error('');
     console.error('Files created:');
-    console.error(`  ${relativePath}/.fozikio/config.yaml`);
+    console.error(`  ${relativePath}/.fozikio/agent.yaml`);
+    console.error(`  ${relativePath}/.fozikio/agent-kit.json`);
+    console.error(`  ${relativePath}/.fozikio/README.md`);
+    console.error(`  ${relativePath}/.fozikio/mind/profile.md`);
+    console.error(`  ${relativePath}/.fozikio/knowledge/_index.md`);
+    console.error(`  ${relativePath}/.fozikio/journal/`);
+    console.error(`  ${relativePath}/.fozikio/state/templates/`);
+    console.error(`  ${relativePath}/.fozikio/credentials/.gitignore`);
     console.error(`  ${relativePath}/.mcp.json`);
     console.error(`  ${relativePath}/CLAUDE.md`);
     console.error(`  ${relativePath}/AGENTS.md`);
@@ -341,14 +430,14 @@ export function runInit(args) {
     }
     if (hasHookifyRules) {
         console.error('');
-        console.error('Recommended hookify rules available. Run `cortex-kit install-rules` to install.');
+        console.error('Recommended hookify rules available. Run `fozikio install-rules` to install.');
     }
     console.error('');
     console.error('Next steps:');
     if (!opts.here) {
         console.error(`  cd ${opts.name}`);
     }
-    console.error(`  # Edit .fozikio/config.yaml to configure your store and providers`);
+    console.error(`  # Edit .fozikio/agent.yaml to configure your store and providers`);
     console.error(`  # Add cortex to your MCP client using .mcp.json`);
     console.error(`  npx cortex-engine   # start the MCP server`);
 }

package/dist/bin/init.js.map

@@ -1 +1 @@
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package/dist/core/types.d.ts

@@ -56,6 +56,7 @@ export interface Edge {
     evidence: string;
     created_at: Date;
 }
+export type ObservationContentType = 'declarative' | 'interrogative' | 'speculative' | 'reflective';
 export interface Observation {
     id: string;
     content: string;
@@ -69,6 +70,8 @@ export interface Observation {
     embedding: number[] | null;
     keywords: string[];
     provenance?: ModelProvenance;
+    /** Content type for filtering — declarative (facts), interrogative (questions), speculative (hypotheses), reflective (synthesis). Defaults to 'declarative'. */
+    content_type?: ObservationContentType;
 }
 export type OpsEntryType = 'log' | 'instruction' | 'handoff' | 'milestone' | 'decision';
 export type OpsStatus = 'active' | 'done' | 'stale';

package/dist/core/types.d.ts.map

@@ -1 +1 @@
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package/dist/engines/cognition.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"cognition.d.ts","sourceRoot":"","sources":["../../src/engines/cognition.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;GAeG;AAEH,OAAO,KAAK,EAAE,WAAW,EAAE,MAAM,kBAAkB,CAAC;AACpD,OAAO,KAAK,EAAE,aAAa,EAAE,MAAM,kBAAkB,CAAC;AACtD,OAAO,KAAK,EAAE,WAAW,EAAE,MAAM,gBAAgB,CAAC;AAOlD,MAAM,WAAW,WAAW;IAC1B,MAAM,EAAE;QACN,OAAO,EAAE;YAAE,SAAS,EAAE,MAAM,CAAC;YAAC,WAAW,EAAE,MAAM,CAAA;SAAE,CAAC;QACpD,MAAM,EAAE;YAAE,OAAO,EAAE,MAAM,CAAA;SAAE,CAAC;QAC5B,MAAM,EAAE;YAAE,OAAO,EAAE,MAAM,CAAA;SAAE,CAAC;QAC5B,OAAO,EAAE;YAAE,gBAAgB,EAAE,MAAM,CAAA;SAAE,CAAC;QACtC,KAAK,EAAE;YAAE,MAAM,EAAE,MAAM,CAAA;SAAE,CAAC;QAC1B,MAAM,EAAE;YAAE,IAAI,EAAE,MAAM,CAAA;SAAE,CAAC;QACzB,QAAQ,EAAE;YAAE,YAAY,EAAE,MAAM,CAAA;SAAE,CAAC;KACpC,CAAC;IACF,eAAe,EAAE,MAAM,CAAC;IACxB,WAAW,EAAE,MAAM,CAAC;IACpB,4CAA4C;IAC5C,gBAAgB,EAAE,MAAM,CAAC;CAC1B;AAED,MAAM,WAAW,YAAY;IAC3B,iEAAiE;IACjE,iBAAiB,CAAC,EAAE,MAAM,CAAC;IAC3B,0DAA0D;IAC1D,YAAY,CAAC,EAAE,MAAM,CAAC;IACtB,yDAAyD;IACzD,oBAAoB,CAAC,EAAE,MAAM,CAAC;IAC9B,0DAA0D;IAC1D,iBAAiB,CAAC,EAAE,MAAM,CAAC;IAC3B,gFAAgF;IAChF,6BAA6B,CAAC,EAAE,MAAM,CAAC;IACvC,uCAAuC;IACvC,gBAAgB,CAAC,EAAE,MAAM,CAAC;IAC1B,sCAAsC;IACtC,eAAe,CAAC,EAAE,MAAM,CAAC;CAC1B;AAiiBD;;;;;;;;GAQG;AACH,wBAAsB,gBAAgB,CACpC,KAAK,EAAE,WAAW,EAClB,KAAK,EAAE,aAAa,EACpB,GAAG,EAAE,WAAW,EAChB,OAAO,GAAE,YAAiB,GACzB,OAAO,CAAC,WAAW,CAAC,CAwDtB"}

package/dist/engines/cognition.js

@@ -137,7 +137,19 @@ async function refineMemories(store, embed, llm, _options) {
 async function createFromUnclustered(store, embed, llm, unclusteredObs, options) {
     const createLimit = options.create_limit ?? 10;
     let created = 0;
-    const candidates = unclusteredObs.slice(0, createLimit);
+    // Only promote declarative observations to memories.
+    // Interrogative (questions) and speculative (hypotheses) stay as observations —
+    // they shouldn't become knowledge nodes in the memory graph.
+    const declarativeObs = unclusteredObs.filter(obs => !obs.content_type || obs.content_type === 'declarative' || obs.content_type === 'reflective');
+    // Mark non-declarative observations as processed so they don't re-enter the pipeline
+    const nonDeclarativeObs = unclusteredObs.filter(obs => obs.content_type === 'interrogative' || obs.content_type === 'speculative');
+    for (const obs of nonDeclarativeObs) {
+        try {
+            await store.markObservationProcessed(obs.id);
+        }
+        catch { /* skip */ }
+    }
+    const candidates = declarativeObs.slice(0, createLimit);
     for (const obs of candidates) {
         try {
             const categoryPrompt = `Classify this text into exactly one category: belief, pattern, entity, topic, value, project, insight, observation.\n\n` +

package/dist/engines/cognition.js.map

@@ -1 +1 @@
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package/dist/index.d.ts

@@ -10,7 +10,7 @@ export type { NLIProvider, NLIResult, NLILabel } from './core/nli.js';
 export type { CortexConfig, AgentConfig, NamespaceConfig, IngestionTriggerConfig, BridgeConfig, BridgeRuleConfig, ModelProvenanceConfig, BenchmarkConfig, } from './core/config.js';
 export { DEFAULT_CONFIG } from './core/config.js';
 export { Session } from './core/session.js';
-export type { Memory, MemorySummary, MemoryCategory, FSRSData, FSRSState, Edge, EdgeRelation, Observation, OpsEntry, OpsEntryType, OpsStatus, OpsFilters, Signal, SignalType, BeliefEntry, SearchResult, ActivationResult, IngestDecision, GateResult, ScheduleResult, ModelProvenance, ConfidenceTier, QueryFilter, } from './core/types.js';
+export type { Memory, MemorySummary, MemoryCategory, FSRSData, FSRSState, Edge, EdgeRelation, Observation, ObservationContentType, OpsEntry, OpsEntryType, OpsStatus, OpsFilters, Signal, SignalType, BeliefEntry, SearchResult, ActivationResult, IngestDecision, GateResult, ScheduleResult, ModelProvenance, ConfidenceTier, QueryFilter, } from './core/types.js';
 export { retrievability, scheduleNext, initialStability, FSRS_WEIGHTS, DESIRED_RETENTION, } from './engines/fsrs.js';
 export { extractKeywords } from './engines/keywords.js';
 export { predictionErrorGate, hydeExpand, spreadActivation, memoryToSummary, SIMILARITY_MERGE, SIMILARITY_LINK, ACTIVATION_DECAY, MAX_ACTIVATION_DEPTH, } from './engines/memory.js';

package/dist/index.d.ts.map

@@ -1 +1 @@
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