symbiote-cli 0.1.1 → 0.1.3

package/README.md

@@ -40,7 +40,8 @@ They're complementary. Use CLAUDE.md for explicit instructions your AI should al
 ## Quick Start
 
 ```bash
-npx symbiote-cli install
+npm install -g symbiote-cli
+symbiote install
 ```
 
 One command. Auto-detects your installed editors (Claude Code, Cursor, Windsurf, Copilot, OpenCode), registers the MCP server globally for each, and sets up 9 Claude Code hooks + the `/symbiote-init` skill. Run it once.
@@ -205,7 +206,7 @@ Every tool call is observed and correlated with the code graph — not raw text
 symbiote serve
 ```
 
-Open `localhost:3333`. Your project's brain — a 3D neural graph of your entire codebase. Nodes are files, functions, classes. Edges are calls, imports, dependencies. Color-coded by module cluster. Sized by PageRank importance.
+Open the URL printed in your terminal. Your project's brain — a 3D neural graph of your entire codebase. Nodes are files, functions, classes. Edges are calls, imports, dependencies. Color-coded by module cluster. Sized by PageRank importance.
 
 **It reacts in real time.** When your AI reads a file, the node glows. When it edits, the node pulses bright. When it navigates between files, impulses fire along the edges. You're watching your AI think.
 
@@ -368,7 +369,7 @@ Symbiote uses Tree-sitter for precise code parsing. **Bundled** languages ship w
 | `symbiote install`      | One-time global setup for all detected editors |
 | `symbiote scan`         | Rescan codebase (incremental)                  |
 | `symbiote scan --force` | Full rescan, ignore cache                      |
-| `symbiote serve`        | MCP server + web UI at localhost:3333          |
+| `symbiote serve`        | MCP server + web UI (port auto-assigned)       |
 | `symbiote mcp`          | MCP server only (stdio, for editors)           |
 | `symbiote dna`          | View and manage developer DNA                  |
 | `symbiote impact`       | Analyze impact of working changes              |

package/dist/src/brain/health/constraint-checker.d.ts

@@ -1,4 +1,3 @@
-import type { Repository } from '#storage/repository.js';
 import type { IntentStore } from '../intent.js';
 import type { ConstraintViolation, DescriptiveConstraint } from './types.js';
 export interface ConstraintCheckResult {
@@ -6,10 +5,9 @@ export interface ConstraintCheckResult {
     descriptive: DescriptiveConstraint[];
 }
 export declare class ConstraintChecker {
-    private repo;
     private intent;
-    constructor(repo: Repository, intent: IntentStore);
-    check(): Promise<ConstraintCheckResult>;
+    constructor(intent: IntentStore);
+    check(allFilePaths: Set<string>): Promise<ConstraintCheckResult>;
     private checkWithPattern;
     private getFilesInScope;
 }

package/dist/src/brain/health/constraint-checker.d.ts.map

@@ -1 +1 @@
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package/dist/src/brain/health/constraint-checker.js

@@ -4,23 +4,16 @@ import { detectLanguage, getGrammar } from '#core/languages.js';
 const require = createRequire(import.meta.url);
 const Parser = require('tree-sitter');
 export class ConstraintChecker {
-    repo;
     intent;
-    constructor(repo, intent) {
-        this.repo = repo;
+    constructor(intent) {
         this.intent = intent;
     }
-    async check() {
+    async check(allFilePaths) {
         const constraints = await this.intent.listEntries('constraint', {
             status: 'active',
         });
         const violations = [];
         const descriptive = [];
-        const allNodes = await this.repo.getAllNodes();
-        const allFilePaths = new Set();
-        for (const node of allNodes) {
-            allFilePaths.add(node.filePath);
-        }
         for (const constraint of constraints) {
             if (constraint.frontmatter.pattern) {
                 const found = await this.checkWithPattern(constraint, allFilePaths);

package/dist/src/brain/health/constraint-checker.js.map

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package/dist/src/brain/health/coupling-analyzer.d.ts

@@ -1,9 +1,6 @@
-import type { Repository } from '#storage/repository.js';
 import type { CouplingHotspot } from './types.js';
 import type { PreFetchedData } from './cycle-detector.js';
 export declare class CouplingAnalyzer {
-    private repo;
-    constructor(repo: Repository);
-    detect(preFetched?: PreFetchedData): Promise<CouplingHotspot[]>;
+    detect(preFetched: PreFetchedData): Promise<CouplingHotspot[]>;
 }
 //# sourceMappingURL=coupling-analyzer.d.ts.map

package/dist/src/brain/health/coupling-analyzer.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"coupling-analyzer.d.ts","sourceRoot":"","sources":["../../../../src/brain/health/coupling-analyzer.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,eAAe,EAAE,MAAM,YAAY,CAAC;AAClD,OAAO,KAAK,EAAE,cAAc,EAAE,MAAM,qBAAqB,CAAC;AAwB1D,qBAAa,gBAAgB;IACnB,MAAM,CAAC,UAAU,EAAE,cAAc,GAAG,OAAO,CAAC,eAAe,EAAE,CAAC;CA8FvE"}

package/dist/src/brain/health/coupling-analyzer.js

@@ -18,13 +18,8 @@ function computeThreshold(weightedCounts) {
     return Math.max(p90, MIN_THRESHOLD);
 }
 export class CouplingAnalyzer {
-    repo;
-    constructor(repo) {
-        this.repo = repo;
-    }
     async detect(preFetched) {
-        const allNodes = preFetched?.nodes ?? (await this.repo.getAllNodes());
-        const allEdges = preFetched?.edges ?? (await this.repo.getAllEdges());
+        const { nodes: allNodes, edges: allEdges } = preFetched;
         if (allEdges.length === 0)
             return [];
         const nodeToFile = new Map();
@@ -36,6 +31,8 @@ export class CouplingAnalyzer {
         const fileFanIn = new Map();
         const fileFanOut = new Map();
         for (const edge of allEdges) {
+            if (edge.type === 'contains')
+                continue;
             const sourceFile = nodeToFile.get(edge.sourceId);
             const targetFile = nodeToFile.get(edge.targetId);
             if (!sourceFile || !targetFile || sourceFile === targetFile) {

package/dist/src/brain/health/coupling-analyzer.js.map

@@ -1 +1 @@
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package/dist/src/brain/health/cycle-detector.d.ts

@@ -1,12 +1,10 @@
-import type { Repository, NodeRecord, EdgeRecord } from '#storage/repository.js';
+import type { NodeRecord, EdgeRecord } from '#storage/repository.js';
 import type { CircularDep } from './types.js';
 export interface PreFetchedData {
     nodes: NodeRecord[];
     edges: EdgeRecord[];
 }
 export declare class CycleDetector {
-    private repo;
-    constructor(repo: Repository);
-    detect(preFetched?: PreFetchedData): Promise<CircularDep[]>;
+    detect(preFetched: PreFetchedData): Promise<CircularDep[]>;
 }
 //# sourceMappingURL=cycle-detector.d.ts.map

package/dist/src/brain/health/cycle-detector.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"cycle-detector.d.ts","sourceRoot":"","sources":["../../../../src/brain/health/cycle-detector.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,UAAU,EAAE,UAAU,EAAE,MAAM,wBAAwB,CAAC;AACrE,OAAO,KAAK,EAAE,WAAW,EAAE,MAAM,YAAY,CAAC;AAE9C,MAAM,WAAW,cAAc;IAC3B,KAAK,EAAE,UAAU,EAAE,CAAC;IACpB,KAAK,EAAE,UAAU,EAAE,CAAC;CACvB;AAED,qBAAa,aAAa;IAChB,MAAM,CAAC,UAAU,EAAE,cAAc,GAAG,OAAO,CAAC,WAAW,EAAE,CAAC;CAqEnE"}

package/dist/src/brain/health/cycle-detector.js

@@ -1,76 +1,61 @@
 export class CycleDetector {
-    repo;
-    constructor(repo) {
-        this.repo = repo;
-    }
     async detect(preFetched) {
-        const allEdges = preFetched?.edges ?? (await this.repo.getAllEdges());
-        if (allEdges.length === 0)
+        const { nodes, edges } = preFetched;
+        if (edges.length === 0)
             return [];
-        const nodeMap = preFetched ? new Map(preFetched.nodes.map((n) => [n.id, n])) : undefined;
-        const adjacency = new Map();
-        for (const edge of allEdges) {
-            if (edge.sourceId === edge.targetId)
+        const nodeToFile = new Map();
+        for (const node of nodes) {
+            nodeToFile.set(node.id, node.filePath);
+        }
+        const fileGraph = new Map();
+        const DEP_EDGE_TYPES = new Set(['imports', 'calls', 'extends']);
+        for (const edge of edges) {
+            if (!DEP_EDGE_TYPES.has(edge.type))
+                continue;
+            const sourceFile = nodeToFile.get(edge.sourceId);
+            const targetFile = nodeToFile.get(edge.targetId);
+            if (!sourceFile || !targetFile || sourceFile === targetFile)
                 continue;
-            if (!adjacency.has(edge.sourceId)) {
-                adjacency.set(edge.sourceId, []);
+            if (!fileGraph.has(sourceFile)) {
+                fileGraph.set(sourceFile, new Set());
             }
-            adjacency.get(edge.sourceId).push(edge.targetId);
+            fileGraph.get(sourceFile).add(targetFile);
         }
         const cycles = [];
         const visited = new Set();
         const inStack = new Set();
         const seen = new Set();
-        const resolveFilePaths = async (chain) => {
-            const filePaths = new Set();
-            for (const id of chain) {
-                if (nodeMap) {
-                    const node = nodeMap.get(id);
-                    if (node)
-                        filePaths.add(node.filePath);
-                }
-                else {
-                    const node = await this.repo.getNodeById(id);
-                    if (node)
-                        filePaths.add(node.filePath);
-                }
-            }
-            return filePaths;
-        };
-        const dfs = async (nodeId, nodePath) => {
-            if (inStack.has(nodeId)) {
-                const cycleStart = nodePath.indexOf(nodeId);
+        const dfs = (file, path) => {
+            if (inStack.has(file)) {
+                const cycleStart = path.indexOf(file);
                 if (cycleStart < 0)
                     return;
-                const chain = nodePath.slice(cycleStart);
-                const filePaths = await resolveFilePaths(chain);
-                if (filePaths.size <= 1)
-                    return;
+                const chain = path.slice(cycleStart);
                 const key = [...chain].sort().join(',');
                 if (seen.has(key))
                     return;
                 seen.add(key);
                 cycles.push({
                     chain,
-                    filePaths: [...filePaths],
+                    filePaths: chain,
                 });
                 return;
             }
-            if (visited.has(nodeId))
+            if (visited.has(file))
                 return;
-            visited.add(nodeId);
-            inStack.add(nodeId);
-            const neighbors = adjacency.get(nodeId) ?? [];
-            nodePath.push(nodeId);
+            visited.add(file);
+            inStack.add(file);
+            const neighbors = fileGraph.get(file) ?? new Set();
+            path.push(file);
             for (const neighbor of neighbors) {
-                await dfs(neighbor, nodePath);
+                dfs(neighbor, path);
             }
-            nodePath.pop();
-            inStack.delete(nodeId);
+            path.pop();
+            inStack.delete(file);
         };
-        for (const nodeId of adjacency.keys()) {
-            if (!visited.has(nodeId)) {
-                await dfs(nodeId, []);
+        for (const file of fileGraph.keys()) {
+            if (!visited.has(file)) {
+                dfs(file, []);
             }
         }
         return cycles;

package/dist/src/brain/health/cycle-detector.js.map

@@ -1 +1 @@
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package/dist/src/brain/health/dead-code-detector.d.ts

@@ -1,9 +1,6 @@
-import type { Repository } from '#storage/repository.js';
 import type { DeadCodeEntry } from './types.js';
 import type { PreFetchedData } from './cycle-detector.js';
 export declare class DeadCodeDetector {
-    private repo;
-    constructor(repo: Repository);
-    detect(preFetched?: PreFetchedData): Promise<DeadCodeEntry[]>;
+    detect(preFetched: PreFetchedData): Promise<DeadCodeEntry[]>;
 }
 //# sourceMappingURL=dead-code-detector.d.ts.map

package/dist/src/brain/health/dead-code-detector.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"dead-code-detector.d.ts","sourceRoot":"","sources":["../../../../src/brain/health/dead-code-detector.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,aAAa,EAAE,MAAM,YAAY,CAAC;AAChD,OAAO,KAAK,EAAE,cAAc,EAAE,MAAM,qBAAqB,CAAC;AAU1D,qBAAa,gBAAgB;IACnB,MAAM,CAAC,UAAU,EAAE,cAAc,GAAG,OAAO,CAAC,aAAa,EAAE,CAAC;CA0DrE"}

package/dist/src/brain/health/dead-code-detector.js

@@ -1,31 +1,19 @@
-const TRACKABLE_KINDS = new Set(['function', 'class', 'method', 'type', 'interface', 'variable']);
+const TRACKABLE_KINDS = new Set(['function', 'class']);
 const ENTRY_POINT_NAMES = new Set(['main', 'cli', 'handler', 'run', 'start', 'app', 'server']);
-function isTestFile(filePath) {
-    return /\/test\/|\.test\.|\.spec\./.test(filePath);
+function isReactComponent(node) {
+    return /\.tsx$/.test(node.filePath) && /^[A-Z]/.test(node.name);
 }
 export class DeadCodeDetector {
-    repo;
-    constructor(repo) {
-        this.repo = repo;
-    }
     async detect(preFetched) {
-        const allNodes = preFetched?.nodes ?? (await this.repo.getAllNodes());
+        const { nodes: allNodes, edges: allEdges } = preFetched;
         if (allNodes.length === 0)
             return [];
-        const allEdges = preFetched?.edges ?? (await this.repo.getAllEdges());
-        const nodeById = new Map(allNodes.map((n) => [n.id, n]));
         const productionInbound = new Set();
         const callerMap = new Map();
         for (const edge of allEdges) {
             if (edge.type === 'contains')
                 continue;
-            const sourceNode = nodeById.get(edge.sourceId);
-            const fromTest = sourceNode
-                ? isTestFile(sourceNode.filePath)
-                : isTestFile(edge.sourceId);
-            if (!fromTest) {
-                productionInbound.add(edge.targetId);
-            }
+            productionInbound.add(edge.targetId);
             let callers = callerMap.get(edge.targetId);
             if (!callers) {
                 callers = new Set();
@@ -42,6 +30,10 @@ export class DeadCodeDetector {
                 continue;
             if (ENTRY_POINT_NAMES.has(node.name))
                 continue;
+            if (node.isExported)
+                continue;
+            if (isReactComponent(node))
+                continue;
             deadSet.add(node.id);
             dead.push({ node, reason: 'No dependents found' });
         }
@@ -55,6 +47,10 @@ export class DeadCodeDetector {
                     continue;
                 if (ENTRY_POINT_NAMES.has(node.name))
                     continue;
+                if (node.isExported)
+                    continue;
+                if (isReactComponent(node))
+                    continue;
                 const callers = callerMap.get(node.id);
                 if (!callers)
                     continue;

package/dist/src/brain/health/dead-code-detector.js.map

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package/dist/src/brain/health/index.d.ts

@@ -1,25 +1,21 @@
-import type { Repository } from '#storage/repository.js';
 import type { SymbioteDB } from '#storage/db.js';
+import type { CortexRepository } from '#cortex/repository.js';
 import type { IntentStore } from '../intent.js';
 import type { HealthReport, HealthSnapshot } from './types.js';
 export declare class HealthEngine {
-    private repo;
+    private cortexRepo;
+    private db;
     private cycleDetector;
     private deadCodeDetector;
     private couplingAnalyzer;
     private constraintChecker;
     private history;
-    constructor(repo: Repository, intent: IntentStore, db: SymbioteDB);
+    constructor(cortexRepo: CortexRepository, intent: IntentStore, db: SymbioteDB);
     analyze(): Promise<HealthReport>;
     saveSnapshot(report: HealthReport): Promise<void>;
     getHistory(limit: number): Promise<HealthSnapshot[]>;
     getLatestSnapshot(): Promise<HealthSnapshot | null>;
+    private fetchGraphData;
 }
 export type { HealthReport, HealthSnapshot, ConstraintViolation, DescriptiveConstraint, CircularDep, DeadCodeEntry, CouplingHotspot, CategoryScore, } from './types.js';
-export { CycleDetector } from './cycle-detector.js';
-export { DeadCodeDetector } from './dead-code-detector.js';
-export { CouplingAnalyzer } from './coupling-analyzer.js';
-export { ConstraintChecker, type ConstraintCheckResult } from './constraint-checker.js';
-export { computeHealthScore, computeCategoryScore } from './scorer.js';
-export { HealthHistory, type SaveSnapshotInput } from './history.js';
 //# sourceMappingURL=index.d.ts.map

package/dist/src/brain/health/index.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../../../src/brain/health/index.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,UAAU,EAAE,MAAM,gBAAgB,CAAC;AACjD,OAAO,KAAK,EAAE,gBAAgB,EAAE,MAAM,uBAAuB,CAAC;AAE9D,OAAO,KAAK,EAAE,WAAW,EAAE,MAAM,cAAc,CAAC;AAChD,OAAO,KAAK,EAAE,YAAY,EAAE,cAAc,EAAE,MAAM,YAAY,CAAC;AA4B/D,qBAAa,YAAY;IACrB,OAAO,CAAC,UAAU,CAAmB;IACrC,OAAO,CAAC,EAAE,CAAa;IACvB,OAAO,CAAC,aAAa,CAAgB;IACrC,OAAO,CAAC,gBAAgB,CAAmB;IAC3C,OAAO,CAAC,gBAAgB,CAAmB;IAC3C,OAAO,CAAC,iBAAiB,CAAoB;IAC7C,OAAO,CAAC,OAAO,CAAgB;gBAEnB,UAAU,EAAE,gBAAgB,EAAE,MAAM,EAAE,WAAW,EAAE,EAAE,EAAE,UAAU;IAUvE,OAAO,IAAI,OAAO,CAAC,YAAY,CAAC;IAuChC,YAAY,CAAC,MAAM,EAAE,YAAY,GAAG,OAAO,CAAC,IAAI,CAAC;IAejD,UAAU,CAAC,KAAK,EAAE,MAAM,GAAG,OAAO,CAAC,cAAc,EAAE,CAAC;IAIpD,iBAAiB,IAAI,OAAO,CAAC,cAAc,GAAG,IAAI,CAAC;YAI3C,cAAc;CA0B/B;AAED,YAAY,EACR,YAAY,EACZ,cAAc,EACd,mBAAmB,EACnB,qBAAqB,EACrB,WAAW,EACX,aAAa,EACb,eAAe,EACf,aAAa,GAChB,MAAM,YAAY,CAAC"}

package/dist/src/brain/health/index.js

@@ -4,28 +4,47 @@ import { CouplingAnalyzer } from './coupling-analyzer.js';
 import { ConstraintChecker } from './constraint-checker.js';
 import { computeHealthScore } from './scorer.js';
 import { HealthHistory } from './history.js';
+function isNonProductionFile(filePath) {
+    return /(^|\/)(?:test|dist|build|coverage|node_modules)\/|\.test\.|\.spec\./.test(filePath);
+}
+const EDGE_TABLES = [
+    { table: 'edges_calls', type: 'calls' },
+    { table: 'edges_imports', type: 'imports' },
+    { table: 'edges_extends', type: 'extends' },
+    { table: 'edges_implements', type: 'implements' },
+    { table: 'edges_contains', type: 'contains' },
+    { table: 'edges_reads', type: 'reads' },
+    { table: 'edges_writes', type: 'writes' },
+    { table: 'edges_returns', type: 'returns' },
+];
 export class HealthEngine {
-    repo;
+    cortexRepo;
+    db;
     cycleDetector;
     deadCodeDetector;
     couplingAnalyzer;
     constraintChecker;
     history;
-    constructor(repo, intent, db) {
-        this.repo = repo;
-        this.cycleDetector = new CycleDetector(repo);
-        this.deadCodeDetector = new DeadCodeDetector(repo);
-        this.couplingAnalyzer = new CouplingAnalyzer(repo);
-        this.constraintChecker = new ConstraintChecker(repo, intent);
+    constructor(cortexRepo, intent, db) {
+        this.cortexRepo = cortexRepo;
+        this.db = db;
+        this.cycleDetector = new CycleDetector();
+        this.deadCodeDetector = new DeadCodeDetector();
+        this.couplingAnalyzer = new CouplingAnalyzer();
+        this.constraintChecker = new ConstraintChecker(intent);
         this.history = new HealthHistory(db);
     }
     async analyze() {
-        const [allNodes, allEdges] = await Promise.all([
-            this.repo.getAllNodes(),
-            this.repo.getAllEdges(),
-        ]);
-        const preFetched = { nodes: allNodes, edges: allEdges };
-        const constraintResult = await this.constraintChecker.check();
+        const [rawNodes, rawEdges] = await this.fetchGraphData();
+        const prodNodes = rawNodes.filter((n) => !isNonProductionFile(n.filePath));
+        const prodNodeIds = new Set(prodNodes.map((n) => n.id));
+        const prodEdges = rawEdges.filter((e) => prodNodeIds.has(e.sourceId) && prodNodeIds.has(e.targetId));
+        const preFetched = { nodes: prodNodes, edges: prodEdges };
+        const allFilePaths = new Set();
+        for (const node of prodNodes) {
+            allFilePaths.add(node.filePath);
+        }
+        const constraintResult = await this.constraintChecker.check(allFilePaths);
         const circularDeps = await this.cycleDetector.detect(preFetched);
         const deadCode = await this.deadCodeDetector.detect(preFetched);
         const couplingHotspots = await this.couplingAnalyzer.detect(preFetched);
@@ -66,11 +85,29 @@ export class HealthEngine {
     async getLatestSnapshot() {
         return this.history.latest();
     }
+    async fetchGraphData() {
+        const symbols = await this.cortexRepo.getAllSymbols();
+        const nodes = symbols.map((s) => ({
+            id: s.id,
+            type: s.kind,
+            name: s.name,
+            filePath: s.filePath,
+            lineStart: s.lineStart,
+            lineEnd: s.lineEnd,
+            isExported: s.isExported,
+        }));
+        const edges = [];
+        for (const { table, type } of EDGE_TABLES) {
+            const rows = await this.db.all(`SELECT source_id, target_id FROM ${table}`);
+            for (const row of rows) {
+                edges.push({
+                    sourceId: row.source_id,
+                    targetId: row.target_id,
+                    type,
+                });
+            }
+        }
+        return [nodes, edges];
+    }
 }
-export { CycleDetector } from './cycle-detector.js';
-export { DeadCodeDetector } from './dead-code-detector.js';
-export { CouplingAnalyzer } from './coupling-analyzer.js';
-export { ConstraintChecker } from './constraint-checker.js';
-export { computeHealthScore, computeCategoryScore } from './scorer.js';
-export { HealthHistory } from './history.js';
 //# sourceMappingURL=index.js.map

package/dist/src/brain/health/index.js.map

@@ -1 +1 @@
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package/dist/src/brain/intent.d.ts

@@ -1,5 +1,6 @@
 export type IntentType = 'decision' | 'constraint';
 export type IntentStatus = 'active' | 'proposed' | 'rejected' | 'superseded';
+export type IntentEnforcement = 'strict' | 'warn';
 export interface IntentFrontmatter {
     id: string;
     type: IntentType;
@@ -8,6 +9,7 @@ export interface IntentFrontmatter {
     author: string;
     createdAt: string;
     pattern?: string;
+    enforcement?: IntentEnforcement;
 }
 export interface IntentEntry {
     frontmatter: IntentFrontmatter;

package/dist/src/brain/intent.d.ts.map

@@ -1 +1 @@
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