symbiote-cli 0.1.1 → 0.1.3

package/dist/src/mcp/server.js

@@ -31,9 +31,16 @@ function textResult(data) {
     return { type: 'text', text: JSON.stringify(data, null, 2) };
 }
 export function createMcpServer(ctx) {
-    const server = new McpServer({
-        name: 'symbiote',
-        version,
+    const server = new McpServer({ name: 'symbiote', version }, {
+        instructions: [
+            'Symbiote provides code intelligence through graph analysis.',
+            'Search for these tools when:',
+            '- Before refactoring or renaming: get_impact, rename_symbol',
+            '- Understanding unfamiliar code: get_context_for_file, get_context_for_symbol',
+            '- Finding code by meaning: semantic_search',
+            '- Reviewing changes before commit: detect_changes',
+            '- Recording developer corrections: record_instruction',
+        ].join('\n'),
     });
     let cachedImpact = null;
     function getImpactAnalyzer() {
@@ -42,7 +49,7 @@ export function createMcpServer(ctx) {
         }
         return cachedImpact;
     }
-    server.tool('get_developer_dna', "Returns the developer's coding style, preferences, and anti-patterns.", {
+    server.tool('get_developer_dna', "Get the developer's coding style and preferences. Call when unsure about conventions.", {
         category: z
             .string()
             .optional()
@@ -54,7 +61,7 @@ export function createMcpServer(ctx) {
     }, async (input) => ({
         content: [textResult(handleGetDeveloperDna(ctx, input))],
     }));
-    server.tool('record_instruction', 'Record a developer correction or coding preference as DNA. Call this whenever the developer corrects your output, states a preference, or gives style guidance. The instruction will be learned and applied in future sessions.', {
+    server.tool('record_instruction', 'When the developer corrects your style or preferences, call this so it persists across sessions.', {
         instruction: z
             .string()
             .describe('The correction or preference to record (e.g., "Use early returns instead of nested else blocks")'),
@@ -68,24 +75,29 @@ export function createMcpServer(ctx) {
             .optional()
             .default(false)
             .describe('True if the developer explicitly asked to record this, false if inferred from a correction'),
+        category: z
+            .enum(['style', 'preferences', 'anti-patterns', 'decisions'])
+            .optional()
+            .describe('Category for this instruction. Provide this so Symbiote does not have to guess.'),
     }, async (input) => {
         const sid = input.sessionId || `session-${Date.now()}`;
         const result = handleRecordInstruction(ctx, {
             instruction: input.instruction,
             sessionId: sid,
             isExplicit: input.isExplicit,
+            category: input.category,
         });
         return { content: [textResult(result)] };
     });
-    server.tool('get_project_overview', "Returns the project's structure, stats, and health summary.", {}, async () => ({
+    server.tool('get_project_overview', 'Get project structure, stats, and active constraints. Use when starting work on an unfamiliar area.', {}, async () => ({
         content: [textResult(await handleGetProjectOverview(ctx))],
     }));
-    server.tool('get_context_for_file', 'Returns everything about a specific file: symbols, dependencies, dependents, constraints, decisions.', {
+    server.tool('get_context_for_file', 'Before refactoring a file, call this to see all dependencies and dependents — prevents breaking downstream code.', {
         filePath: z.string().describe('The file path to get context for'),
     }, async (input) => ({
         content: [textResult(await handleGetContextForFile(ctx, input))],
     }));
-    server.tool('query_graph', 'Query the code graph using SQL/PGQ or plain SQL. Accepts any read-only SELECT query against cortex tables and the code_graph property graph.', {
+    server.tool('query_graph', 'Advanced: raw SQL against the code graph. Prefer get_context_for_file or get_context_for_symbol for common lookups.', {
         query: z.string().describe('SQL or SQL/PGQ query (read-only SELECT only)'),
         type: z
             .enum(['search', 'dependencies', 'dependents', 'hubs'])
@@ -105,16 +117,16 @@ export function createMcpServer(ctx) {
         const result = await handleQueryGraphV2({ db: ctx.db, cortexRepo: ctx.cortexRepo }, { query: input.query });
         return { content: [textResult(result)] };
     });
-    server.tool('semantic_search', 'Natural language search over the codebase using vector embeddings.', {
+    server.tool('semantic_search', "Find code by meaning, not keywords. Use when looking for functionality but don't know exact names or locations.", {
         query: z.string().describe("Natural language description of what you're looking for"),
         limit: z.number().optional().default(10).describe('Maximum number of results'),
     }, async (input) => ({
         content: [textResult(await handleSemanticSearch(ctx, input))],
     }));
-    server.tool('get_health', "Returns the project's health report: dead code, circular deps, orphans, violations.", {}, async () => ({
+    server.tool('get_health', 'Get actionable health issues: circular dependencies, dead code, coupling hotspots. Use before major changes.', {}, async () => ({
         content: [textResult(await handleGetHealth(ctx))],
     }));
-    server.tool('get_impact', 'Analyze blast radius: what breaks if a given symbol changes. Returns affected nodes grouped by depth with confidence scores.', {
+    server.tool('get_impact', 'Before changing a shared function or class, see every file affected with confidence scores. Essential for safe refactoring.', {
         target: z
             .string()
             .describe('Node ID of the symbol to analyze (e.g., fn:auth.ts:login)'),
@@ -127,7 +139,7 @@ export function createMcpServer(ctx) {
         const result = await handleGetImpact({ graph: ctx.graphology, impact: getImpactAnalyzer(), cortexRepo: ctx.cortexRepo }, input);
         return { content: [textResult(result)] };
     });
-    server.tool('detect_changes', 'Analyze uncommitted git changes: maps modified files to affected modules with risk assessment.', {}, async () => {
+    server.tool('detect_changes', 'Map uncommitted git changes to affected modules with risk levels. Use before committing or creating PRs.', {}, async () => {
         const result = await handleDetectChanges({ graph: ctx.graphology, impact: getImpactAnalyzer(), cortexRepo: ctx.cortexRepo }, {});
         return { content: [textResult(result)] };
     });
@@ -165,7 +177,7 @@ export function createMcpServer(ctx) {
         ],
     }));
     registerTraceTools(server, ctx.cortexRepo);
-    server.tool('find_patterns', 'Detect anti-patterns, architectural violations, and complexity hotspots within a scope', {
+    server.tool('find_patterns', 'Detect anti-patterns and complexity hotspots in a scope. Use during code review or when investigating quality.', {
         scope: z.string().describe('Scope to search: file path, directory, or "all"'),
         kinds: z
             .array(z.enum([
@@ -191,11 +203,11 @@ export function createMcpServer(ctx) {
         const result = await handleFindPatterns(ctx.cortexRepo, input);
         return { content: [textResult(result)] };
     });
-    server.tool('get_architecture', 'Get detected architectural layers, boundaries, dependency direction, and violation summary', {}, async () => {
+    server.tool('get_architecture', 'Understand module structure: layers, boundaries, dependency violations. Use when working across module boundaries.', {}, async () => {
         const result = await handleGetArchitecture(ctx.cortexRepo);
         return { content: [textResult(result)] };
     });
-    server.tool('get_context_for_symbol', 'Deep dive into one function, class, or method: callers, callees, type relationships, import references.', {
+    server.tool('get_context_for_symbol', 'Deep dive into a function or class: callers, callees, type relationships. Use before modifying shared code.', {
         symbol: z
             .string()
             .describe('Symbol name or ID (e.g., "validateEmail" or "fn:utils.ts:validateEmail")'),
@@ -203,7 +215,7 @@ export function createMcpServer(ctx) {
         const result = await handleGetContextForSymbol({ db: ctx.db, cortexRepo: ctx.cortexRepo }, input);
         return { content: [textResult(result)] };
     });
-    server.tool('rename_symbol', 'Graph-aware multi-file rename preview. Returns a diff — does NOT write to disk.', {
+    server.tool('rename_symbol', "Safe rename across the codebase — shows every file that needs to change. Returns a preview, doesn't write.", {
         symbol: z.string().describe('Symbol name or ID to rename'),
         new_name: z.string().describe('New name for the symbol'),
         scope: z
@@ -216,7 +228,7 @@ export function createMcpServer(ctx) {
         const result = await handleRenameSymbol({ cortexRepo: ctx.cortexRepo, rootDir: ctx.rootDir }, { ...rest, newName });
         return { content: [textResult(result)] };
     });
-    server.tool('get_constraints', 'Returns active project constraints — rules the codebase enforces.', {
+    server.tool('get_constraints', 'List active architectural rules scoped to a directory or the whole project.', {
         scope: z
             .string()
             .optional()
@@ -225,7 +237,7 @@ export function createMcpServer(ctx) {
         const result = await handleGetConstraints(ctx, input);
         return { content: [textResult(result)] };
     });
-    server.tool('get_decisions', 'Returns architectural decisions — choices made with rationale.', {
+    server.tool('get_decisions', 'List architectural decisions with rationale. Use to understand why something was built a certain way.', {
         scope: z
             .string()
             .optional()
@@ -234,7 +246,7 @@ export function createMcpServer(ctx) {
         const result = await handleGetDecisions(ctx, input);
         return { content: [textResult(result)] };
     });
-    server.tool('propose_constraint', 'Propose a new project constraint. Status starts as "proposed" for developer review.', {
+    server.tool('propose_constraint', 'Suggest a new architectural rule for developer review.', {
         id: z.string().describe('Unique constraint ID (slug format, e.g. "no-raw-sql")'),
         content: z.string().describe('The constraint rule text'),
         scope: z
@@ -246,7 +258,7 @@ export function createMcpServer(ctx) {
         const result = handleProposeConstraint(ctx, input);
         return { content: [textResult(result)] };
     });
-    server.tool('propose_decision', 'Record an architectural decision with rationale. Status starts as "proposed" for developer review.', {
+    server.tool('propose_decision', 'Record an architectural decision with rationale for developer review.', {
         id: z
             .string()
             .describe('Unique decision ID (slug format, e.g. "chose-vitest-over-jest")'),

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package/dist/src/mcp/tools/dna-tools.d.ts

@@ -13,6 +13,7 @@ export interface RecordInstructionInput {
     instruction: string;
     sessionId: string;
     isExplicit: boolean;
+    category?: string;
 }
 export interface RecordInstructionOutput {
     entry: DnaEntry;

package/dist/src/mcp/tools/dna-tools.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"dna-tools.d.ts","sourceRoot":"","sources":["../../../../src/mcp/tools/dna-tools.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,aAAa,EAAE,MAAM,eAAe,CAAC;AACnD,OAAO,KAAK,EAAE,QAAQ,EAAe,MAAM,eAAe,CAAC;AAE3D,OAAO,KAAK,EAAE,YAAY,EAAE,MAAM,kBAAkB,CAAC;AAGrD,MAAM,WAAW,oBAAoB;IACjC,QAAQ,CAAC,EAAE,MAAM,CAAC;IAClB,WAAW,CAAC,EAAE,MAAM,CAAC;CACxB;AAED,MAAM,WAAW,qBAAqB;IAClC,OAAO,EAAE,QAAQ,EAAE,CAAC;CACvB;AAED,wBAAgB,qBAAqB,CACjC,GAAG,EAAE,aAAa,EAClB,KAAK,EAAE,oBAAoB,GAC5B,YAAY,CAAC,qBAAqB,CAAC,CAUrC;AAED,MAAM,WAAW,sBAAsB;IACnC,WAAW,EAAE,MAAM,CAAC;IACpB,SAAS,EAAE,MAAM,CAAC;IAClB,UAAU,EAAE,OAAO,CAAC;IACpB,QAAQ,CAAC,EAAE,MAAM,CAAC;CACrB;AAED,MAAM,WAAW,uBAAuB;IACpC,KAAK,EAAE,QAAQ,CAAC;CACnB;AAED,wBAAgB,uBAAuB,CACnC,GAAG,EAAE,aAAa,EAClB,KAAK,EAAE,sBAAsB,GAC9B,YAAY,CAAC,uBAAuB,CAAC,CAcvC"}

package/dist/src/mcp/tools/dna-tools.js

@@ -1,3 +1,4 @@
+import { DNA_CATEGORIES } from '#dna/types.js';
 import { wrapResponse } from '../tool-response.js';
 export function handleGetDeveloperDna(ctx, input) {
     let entries = ctx.dnaEngine.getActiveEntries();
@@ -9,7 +10,10 @@ export function handleGetDeveloperDna(ctx, input) {
 }
 export function handleRecordInstruction(ctx, input) {
     const source = input.isExplicit ? 'explicit' : 'correction';
-    const entry = ctx.dnaEngine.captureInstruction(input.instruction, input.sessionId, source);
+    const validCategory = input.category && DNA_CATEGORIES.includes(input.category)
+        ? input.category
+        : undefined;
+    const entry = ctx.dnaEngine.captureInstruction(input.instruction, input.sessionId, source, validCategory);
     return wrapResponse({ entry }, 7, false);
 }
 //# sourceMappingURL=dna-tools.js.map

package/dist/src/mcp/tools/dna-tools.js.map

@@ -1 +1 @@
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+{"version":3,"file":"dna-tools.js","sourceRoot":"","sources":["../../../../src/mcp/tools/dna-tools.ts"],"names":[],"mappings":"AAEA,OAAO,EAAE,cAAc,EAAE,MAAM,eAAe,CAAC;AAE/C,OAAO,EAAE,YAAY,EAAE,MAAM,qBAAqB,CAAC;AAWnD,MAAM,UAAU,qBAAqB,CACjC,GAAkB,EAClB,KAA2B;IAE3B,IAAI,OAAO,GAAG,GAAG,CAAC,SAAS,CAAC,gBAAgB,EAAE,CAAC;IAE/C,IAAI,KAAK,CAAC,QAAQ,EAAE,CAAC;QACjB,OAAO,GAAG,OAAO,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,WAAW,CAAC,QAAQ,KAAK,KAAK,CAAC,QAAQ,CAAC,CAAC;IAC/E,CAAC;IAED,OAAO,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,WAAW,CAAC,UAAU,GAAG,CAAC,CAAC,WAAW,CAAC,UAAU,CAAC,CAAC;IAE5E,OAAO,YAAY,CAAC,EAAE,OAAO,EAAE,EAAE,CAAC,EAAE,KAAK,CAAC,CAAC;AAC/C,CAAC;AAaD,MAAM,UAAU,uBAAuB,CACnC,GAAkB,EAClB,KAA6B;IAE7B,MAAM,MAAM,GAAG,KAAK,CAAC,UAAU,CAAC,CAAC,CAAC,UAAU,CAAC,CAAC,CAAC,YAAY,CAAC;IAC5D,MAAM,aAAa,GACf,KAAK,CAAC,QAAQ,IAAK,cAAoC,CAAC,QAAQ,CAAC,KAAK,CAAC,QAAQ,CAAC;QAC5E,CAAC,CAAE,KAAK,CAAC,QAAwB;QACjC,CAAC,CAAC,SAAS,CAAC;IACpB,MAAM,KAAK,GAAG,GAAG,CAAC,SAAS,CAAC,kBAAkB,CAC1C,KAAK,CAAC,WAAW,EACjB,KAAK,CAAC,SAAS,EACf,MAAM,EACN,aAAa,CAChB,CAAC;IAEF,OAAO,YAAY,CAAC,EAAE,KAAK,EAAE,EAAE,CAAC,EAAE,KAAK,CAAC,CAAC;AAC7C,CAAC"}

package/dist/src/mcp/tools/trace-tools.d.ts

@@ -1,4 +1,38 @@
 import type { McpServer } from '@modelcontextprotocol/sdk/server/mcp.js';
 import type { CortexRepository } from '#cortex/repository.js';
+interface SymbolInfo {
+    id: string;
+    name: string;
+    filePath: string;
+    lineStart: number;
+    lineEnd: number;
+    kind: string;
+}
+interface FlowStep {
+    symbolId: string;
+    symbol: SymbolInfo | null;
+    depth: number;
+    edgeType: string;
+    isAsync: boolean;
+    confidence: number;
+}
+interface DataFlowStep {
+    symbolId: string;
+    symbol: SymbolInfo | null;
+    depth: number;
+    direction: 'forward' | 'backward';
+    transform: string | null;
+    confidence: number;
+}
+interface Implementor {
+    symbolId: string;
+    symbol: SymbolInfo | null;
+    confidence: number;
+    isIndirect: boolean;
+}
+export declare function traceExecutionFlow(repo: CortexRepository, entryPoint: string, maxDepth: number, includeAsync: boolean, includeErrors: boolean): Promise<FlowStep[]>;
+export declare function traceDataFlow(repo: CortexRepository, symbol: string, direction: 'forward' | 'backward', maxDepth: number): Promise<DataFlowStep[]>;
+export declare function findImplementors(repo: CortexRepository, interfaceName: string, includeIndirect: boolean): Promise<Implementor[]>;
 export declare function registerTraceTools(server: McpServer, repo: CortexRepository): void;
+export {};
 //# sourceMappingURL=trace-tools.d.ts.map

package/dist/src/mcp/tools/trace-tools.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"trace-tools.d.ts","sourceRoot":"","sources":["../../../../src/mcp/tools/trace-tools.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,SAAS,EAAE,MAAM,yCAAyC,CAAC;AAEzE,OAAO,KAAK,EAAE,gBAAgB,EAAE,MAAM,uBAAuB,CAAC;AAE9D,UAAU,UAAU;IAChB,EAAE,EAAE,MAAM,CAAC;IACX,IAAI,EAAE,MAAM,CAAC;IACb,QAAQ,EAAE,MAAM,CAAC;IACjB,SAAS,EAAE,MAAM,CAAC;IAClB,OAAO,EAAE,MAAM,CAAC;IAChB,IAAI,EAAE,MAAM,CAAC;CAChB;AAED,UAAU,QAAQ;IACd,QAAQ,EAAE,MAAM,CAAC;IACjB,MAAM,EAAE,UAAU,GAAG,IAAI,CAAC;IAC1B,KAAK,EAAE,MAAM,CAAC;IACd,QAAQ,EAAE,MAAM,CAAC;IACjB,OAAO,EAAE,OAAO,CAAC;IACjB,UAAU,EAAE,MAAM,CAAC;CACtB;AAED,UAAU,YAAY;IAClB,QAAQ,EAAE,MAAM,CAAC;IACjB,MAAM,EAAE,UAAU,GAAG,IAAI,CAAC;IAC1B,KAAK,EAAE,MAAM,CAAC;IACd,SAAS,EAAE,SAAS,GAAG,UAAU,CAAC;IAClC,SAAS,EAAE,MAAM,GAAG,IAAI,CAAC;IACzB,UAAU,EAAE,MAAM,CAAC;CACtB;AAED,UAAU,WAAW;IACjB,QAAQ,EAAE,MAAM,CAAC;IACjB,MAAM,EAAE,UAAU,GAAG,IAAI,CAAC;IAC1B,UAAU,EAAE,MAAM,CAAC;IACnB,UAAU,EAAE,OAAO,CAAC;CACvB;AAYD,wBAAsB,kBAAkB,CACpC,IAAI,EAAE,gBAAgB,EACtB,UAAU,EAAE,MAAM,EAClB,QAAQ,EAAE,MAAM,EAChB,YAAY,EAAE,OAAO,EACrB,aAAa,EAAE,OAAO,GACvB,OAAO,CAAC,QAAQ,EAAE,CAAC,CA6GrB;AAED,wBAAsB,aAAa,CAC/B,IAAI,EAAE,gBAAgB,EACtB,MAAM,EAAE,MAAM,EACd,SAAS,EAAE,SAAS,GAAG,UAAU,EACjC,QAAQ,EAAE,MAAM,GACjB,OAAO,CAAC,YAAY,EAAE,CAAC,CA8DzB;AAED,wBAAsB,gBAAgB,CAClC,IAAI,EAAE,gBAAgB,EACtB,aAAa,EAAE,MAAM,EACrB,eAAe,EAAE,OAAO,GACzB,OAAO,CAAC,WAAW,EAAE,CAAC,CAyCxB;AAMD,wBAAgB,kBAAkB,CAAC,MAAM,EAAE,SAAS,EAAE,IAAI,EAAE,gBAAgB,GAAG,IAAI,CAgFlF"}

package/dist/src/mcp/tools/trace-tools.js

@@ -8,7 +8,7 @@ async function resolveSymbol(repo, nameOrId) {
         return byName[0];
     return null;
 }
-async function traceExecutionFlow(repo, entryPoint, maxDepth, includeAsync, includeErrors) {
+export async function traceExecutionFlow(repo, entryPoint, maxDepth, includeAsync, includeErrors) {
     const resolved = await resolveSymbol(repo, entryPoint);
     if (!resolved)
         return [];
@@ -113,7 +113,7 @@ async function traceExecutionFlow(repo, entryPoint, maxDepth, includeAsync, incl
     }
     return steps;
 }
-async function traceDataFlow(repo, symbol, direction, maxDepth) {
+export async function traceDataFlow(repo, symbol, direction, maxDepth) {
     const resolved = await resolveSymbol(repo, symbol);
     if (!resolved)
         return [];
@@ -172,7 +172,7 @@ async function traceDataFlow(repo, symbol, direction, maxDepth) {
     }
     return steps;
 }
-async function findImplementors(repo, interfaceName, includeIndirect) {
+export async function findImplementors(repo, interfaceName, includeIndirect) {
     const resolved = await resolveSymbol(repo, interfaceName);
     if (!resolved)
         return [];
@@ -214,7 +214,7 @@ function textResult(data) {
     return { type: 'text', text: JSON.stringify(data, null, 2) };
 }
 export function registerTraceTools(server, repo) {
-    server.tool('trace_flow', 'Trace execution flow from an entry point through calls and data flows.', {
+    server.tool('trace_flow', 'Follow execution from an entry point through call chains. Use when debugging or understanding how a feature works end-to-end.', {
         entryPoint: z.string().describe('Symbol ID or name to start tracing from'),
         maxDepth: z
             .number()
@@ -236,7 +236,7 @@ export function registerTraceTools(server, repo) {
             textResult(await traceExecutionFlow(repo, input.entryPoint, input.maxDepth, input.includeAsync, input.includeErrors)),
         ],
     }));
-    server.tool('trace_data', 'Trace data flow forward or backward from a symbol.', {
+    server.tool('trace_data', 'Track how data moves through the codebase from a symbol. Use when investigating data transformation bugs or tracing inputs to outputs.', {
         symbol: z.string().describe('Symbol ID or name to trace data flow from'),
         direction: z
             .enum(['forward', 'backward'])
@@ -252,7 +252,7 @@ export function registerTraceTools(server, repo) {
             textResult(await traceDataFlow(repo, input.symbol, input.direction, input.maxDepth)),
         ],
     }));
-    server.tool('find_implementations', 'Find all classes that implement an interface or extend a base class.', {
+    server.tool('find_implementations', 'Find all classes implementing an interface or extending a base class. Use before modifying contracts to see every affected implementation.', {
         interfaceName: z.string().describe('Interface or base class name/ID'),
         includeIndirect: z
             .boolean()

package/dist/src/mcp/tools/trace-tools.js.map

@@ -1 +1 @@
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package/dist/src/storage/repository.d.ts

@@ -6,6 +6,7 @@ export interface NodeRecord {
     filePath: string;
     lineStart: number;
     lineEnd: number;
+    isExported?: boolean;
     metadata?: Record<string, unknown>;
 }
 export interface EdgeRecord {

package/dist/src/storage/repository.d.ts.map

@@ -1 +1 @@
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