spec-gen-cli 1.2.5 → 1.2.7

package/dist/core/services/mcp-handlers/semantic.js

@@ -20,11 +20,16 @@ export function classifyRole(fanIn, fanOut, isHub, isEntryPoint) {
 }
 export function deriveStrategy(role) {
     switch (role) {
-        case 'entry_point': return 'extend_entry_point';
-        case 'orchestrator': return 'add_orchestration_step';
-        case 'hub': return 'cross_cutting_hook';
-        case 'utility': return 'extract_shared_logic';
-        default: return 'call_alongside';
+        case 'entry_point':
+            return 'extend_entry_point';
+        case 'orchestrator':
+            return 'add_orchestration_step';
+        case 'hub':
+            return 'cross_cutting_hook';
+        case 'utility':
+            return 'extract_shared_logic';
+        default:
+            return 'call_alongside';
     }
 }
 export function buildReason(name, role, strategy, fanIn, fanOut) {
@@ -107,9 +112,9 @@ export async function handleSearchCode(directory, query, limit = 10, language, m
     let calleeMap;
     if (llmCtx?.callGraph) {
         const cg = llmCtx.callGraph;
-        const nodeMap = new Map(cg.nodes.map(n => [n.id, n]));
-        callerMap = new Map(cg.nodes.map(n => [n.id, []]));
-        calleeMap = new Map(cg.nodes.map(n => [n.id, []]));
+        const nodeMap = new Map(cg.nodes.map((n) => [n.id, n]));
+        callerMap = new Map(cg.nodes.map((n) => [n.id, []]));
+        calleeMap = new Map(cg.nodes.map((n) => [n.id, []]));
         for (const e of cg.edges) {
             if (!e.calleeId)
                 continue;
@@ -123,7 +128,7 @@ export async function handleSearchCode(directory, query, limit = 10, language, m
     }
     const specPeers = [];
     if (mappingIdx) {
-        const resultFileSet = new Set(results.map(r => r.record.filePath));
+        const resultFileSet = new Set(results.map((r) => r.record.filePath));
         const seedDomains = new Set();
         for (const r of results) {
             for (const spec of specsForFile(mappingIdx, r.record.filePath))
@@ -143,9 +148,13 @@ export async function handleSearchCode(directory, query, limit = 10, language, m
     return {
         query,
         searchMode,
-        ...(searchMode === 'bm25_fallback' ? { note: 'Embedding server unavailable — results based on keyword matching only. Configure EMBED_BASE_URL + EMBED_MODEL for semantic search.' } : {}),
+        ...(searchMode === 'bm25_fallback'
+            ? {
+                note: 'Embedding server unavailable — results based on keyword matching only. Configure EMBED_BASE_URL + EMBED_MODEL for semantic search.',
+            }
+            : {}),
         count: results.length,
-        results: results.map(r => ({
+        results: results.map((r) => ({
             score: r.score,
             name: r.record.name,
             filePath: r.record.filePath,
@@ -186,11 +195,15 @@ export async function handleSuggestInsertionPoints(directory, description, limit
     catch {
         const cfg = await readSpecGenConfig(absDir);
         if (!cfg) {
-            return { error: 'No embedding configuration found. Set EMBED_BASE_URL and EMBED_MODEL env vars, or add an "embedding" section to .spec-gen/config.json.' };
+            return {
+                error: 'No embedding configuration found. Set EMBED_BASE_URL and EMBED_MODEL env vars, or add an "embedding" section to .spec-gen/config.json.',
+            };
         }
         const svcFromConfig = EmbeddingService.fromConfig(cfg);
         if (!svcFromConfig) {
-            return { error: 'No embedding configuration found. Set EMBED_BASE_URL and EMBED_MODEL env vars, or add an "embedding" section to .spec-gen/config.json.' };
+            return {
+                error: 'No embedding configuration found. Set EMBED_BASE_URL and EMBED_MODEL env vars, or add an "embedding" section to .spec-gen/config.json.',
+            };
         }
         embedSvc = svcFromConfig;
     }
@@ -201,9 +214,9 @@ export async function handleSuggestInsertionPoints(directory, description, limit
         readCachedContext(absDir),
     ]);
     // Normalise search scores to [0, 1] for compositeScore (scores are RRF/BM25: higher = better)
-    const maxScore = rawResults.length > 0 ? Math.max(...rawResults.map(r => r.score)) : 1;
-    const normalise = (s) => maxScore > 0 ? s / maxScore : 0;
-    const candidates = rawResults.map(r => {
+    const maxScore = rawResults.length > 0 ? Math.max(...rawResults.map((r) => r.score)) : 1;
+    const normalise = (s) => (maxScore > 0 ? s / maxScore : 0);
+    const candidates = rawResults.map((r) => {
         const role = classifyRole(r.record.fanIn, r.record.fanOut, r.record.isHub, r.record.isEntryPoint);
         const strategy = deriveStrategy(role);
         const score = compositeScore(normalise(r.score), role);
@@ -217,10 +230,13 @@ export async function handleSuggestInsertionPoints(directory, description, limit
             language: r.record.language,
             signature: r.record.signature || undefined,
             docstring: r.record.docstring || undefined,
-            role, insertionStrategy: strategy,
+            role,
+            insertionStrategy: strategy,
             reason: buildReason(r.record.name, role, strategy, r.record.fanIn, r.record.fanOut),
-            fanIn: r.record.fanIn, fanOut: r.record.fanOut,
-            isHub: r.record.isHub, isEntryPoint: r.record.isEntryPoint,
+            fanIn: r.record.fanIn,
+            fanOut: r.record.fanOut,
+            isHub: r.record.isHub,
+            isEntryPoint: r.record.isEntryPoint,
         };
     });
     // RIG-13 — Graph expansion: add depth-1 callers of semantic seed functions.
@@ -228,7 +244,7 @@ export async function handleSuggestInsertionPoints(directory, description, limit
     // they coordinate the domain logic and control the execution flow.
     if (llmCtx?.callGraph) {
         const cg = llmCtx.callGraph;
-        const nodeById = new Map(cg.nodes.map(n => [n.id, n]));
+        const nodeById = new Map(cg.nodes.map((n) => [n.id, n]));
         // Build callerOf: nodeId → caller node ids
         const callerOf = new Map();
         for (const e of cg.edges) {
@@ -238,8 +254,8 @@ export async function handleSuggestInsertionPoints(directory, description, limit
             list.push(e.callerId);
             callerOf.set(e.calleeId, list);
         }
-        const seedIds = new Set(rawResults.map(r => r.record.id));
-        const existingIds = new Set(candidates.map(c => `${c.filePath}::${c.name}`));
+        const seedIds = new Set(rawResults.map((r) => r.record.id));
+        const existingIds = new Set(candidates.map((c) => `${c.filePath}::${c.name}`));
         for (const seedResult of rawResults) {
             const callerIds = callerOf.get(seedResult.record.id) ?? [];
             for (const callerId of callerIds) {
@@ -264,10 +280,13 @@ export async function handleSuggestInsertionPoints(directory, description, limit
                     language: callerNode.language,
                     signature: undefined,
                     docstring: undefined,
-                    role, insertionStrategy: strategy,
+                    role,
+                    insertionStrategy: strategy,
                     reason: `${callerNode.name} calls ${seedResult.record.name} (semantically close to your feature). Adding logic here propagates to the domain.`,
-                    fanIn: callerNode.fanIn, fanOut: callerNode.fanOut,
-                    isHub: false, isEntryPoint: false,
+                    fanIn: callerNode.fanIn,
+                    fanOut: callerNode.fanOut,
+                    isHub: false,
+                    isEntryPoint: false,
                 });
             }
         }
@@ -284,7 +303,9 @@ export async function handleSuggestInsertionPoints(directory, description, limit
                 `Run get_subgraph on "${top[0].name}" to understand its call neighborhood`,
                 `After implementing, run check_spec_drift to verify the code matches the spec`,
             ]
-            : ['No candidates found. Try a broader description or run "spec-gen analyze --embed" to build the index.'],
+            : [
+                'No candidates found. Try a broader description or run "spec-gen analyze --embed" to build the index.',
+            ],
     };
 }
 /**
@@ -297,7 +318,9 @@ export async function handleGetSpec(directory, domain) {
     const absDir = await validateDirectory(directory);
     const specFile = pjoin(absDir, 'openspec', 'specs', domain, 'spec.md');
     if (!existsSync(specFile)) {
-        return { error: `No spec found for domain "${domain}". Run list_spec_domains to see available domains.` };
+        return {
+            error: `No spec found for domain "${domain}". Run list_spec_domains to see available domains.`,
+        };
     }
     const [content, mappingIdx] = await Promise.all([
         readFile(specFile, 'utf-8'),
@@ -321,7 +344,10 @@ export async function handleListSpecDomains(directory) {
     const absDir = await validateDirectory(directory);
     const specsDir = pjoin(absDir, OPENSPEC_DIR, OPENSPEC_SPECS_SUBDIR);
     if (!(await fileExists(specsDir))) {
-        return { domains: [], note: 'No openspec/specs/ directory found. Run "spec-gen generate" first.' };
+        return {
+            domains: [],
+            note: 'No openspec/specs/ directory found. Run "spec-gen generate" first.',
+        };
     }
     let entries;
     try {
@@ -330,7 +356,7 @@ export async function handleListSpecDomains(directory) {
     catch {
         return { domains: [] };
     }
-    const domainChecks = await Promise.all(entries.map(e => fileExists(pjoin(specsDir, e, 'spec.md'))));
+    const domainChecks = await Promise.all(entries.map((e) => fileExists(pjoin(specsDir, e, 'spec.md'))));
     const domains = entries.filter((_, i) => domainChecks[i]);
     return { domains, count: domains.length };
 }
@@ -356,11 +382,15 @@ export async function handleSearchSpecs(directory, query, limit = 10, domain, se
     catch {
         const cfg = await readSpecGenConfig(absDir);
         if (!cfg) {
-            return { error: 'No embedding configuration found. Set EMBED_BASE_URL and EMBED_MODEL env vars, or add an "embedding" section to .spec-gen/config.json.' };
+            return {
+                error: 'No embedding configuration found. Set EMBED_BASE_URL and EMBED_MODEL env vars, or add an "embedding" section to .spec-gen/config.json.',
+            };
         }
         const svcFromConfig = EmbeddingService.fromConfig(cfg);
         if (!svcFromConfig) {
-            return { error: 'No embedding configuration found. Set EMBED_BASE_URL and EMBED_MODEL env vars, or add an "embedding" section to .spec-gen/config.json.' };
+            return {
+                error: 'No embedding configuration found. Set EMBED_BASE_URL and EMBED_MODEL env vars, or add an "embedding" section to .spec-gen/config.json.',
+            };
         }
         embedSvc = svcFromConfig;
     }
@@ -372,7 +402,7 @@ export async function handleSearchSpecs(directory, query, limit = 10, domain, se
     return {
         query,
         count: results.length,
-        results: results.map(r => ({
+        results: results.map((r) => ({
             score: r.score,
             id: r.record.id,
             domain: r.record.domain,
@@ -384,4 +414,43 @@ export async function handleSearchSpecs(directory, query, limit = 10, domain, se
         })),
     };
 }
+/**
+ * Unified search that combines code and spec indexes with cross-scoring
+ */
+export async function handleUnifiedSearch(directory, query, limit = 10, language, domain, section) {
+    const absDir = await validateDirectory(directory);
+    const outputDir = join(absDir, SPEC_GEN_DIR, SPEC_GEN_ANALYSIS_SUBDIR);
+    const { UnifiedSearch, unifiedSearchAvailable } = await import('../../analyzer/unified-search.js');
+    const { EmbeddingService } = await import('../../analyzer/embedding-service.js');
+    if (!(await unifiedSearchAvailable(outputDir))) {
+        return {
+            error: 'No unified search available. Run "spec-gen analyze --embed" first, ' +
+                'then configure EMBED_BASE_URL and EMBED_MODEL.',
+        };
+    }
+    // Resolve embedding service
+    let embedSvc = null;
+    try {
+        embedSvc = EmbeddingService.fromEnv();
+    }
+    catch {
+        const cfg = await readSpecGenConfig(absDir);
+        const svcFromConfig = cfg ? EmbeddingService.fromConfig(cfg) : null;
+        if (svcFromConfig) {
+            embedSvc = svcFromConfig;
+        }
+    }
+    limit = Math.max(1, Math.min(limit, 50));
+    const results = await UnifiedSearch.unifiedSearch(outputDir, query, embedSvc, {
+        limit,
+        language,
+        domain,
+        section,
+    });
+    return {
+        query,
+        count: results.length,
+        results,
+    };
+}
 //# sourceMappingURL=semantic.js.map

package/dist/core/services/mcp-handlers/semantic.js.map

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package/dist/types/index.d.ts

@@ -31,7 +31,7 @@ export interface AnalysisConfig {
     excludePatterns: string[];
 }
 export interface GenerationConfig {
-    provider?: 'anthropic' | 'openai' | 'openai-compat' | 'copilot' | 'gemini' | 'claude-code' | 'mistral-vibe';
+    provider?: 'anthropic' | 'openai' | 'openai-compat' | 'copilot' | 'gemini' | 'claude-code' | 'mistral-vibe' | 'gemini-cli' | 'cursor-agent';
     model?: string;
     openaiCompatBaseUrl?: string;
     skipSslVerify?: boolean;
@@ -251,4 +251,73 @@ export interface SpecMap {
     domainCount: number;
     totalMappedFiles: number;
 }
+export interface SpecSnapshotDomain {
+    name: string;
+    specFile: string;
+    sourceFiles: string[];
+    requirementCount: number;
+    mappedFunctionCount: number;
+    coveragePct: number;
+    specModifiedAt: string;
+    sourcesModifiedAt: string;
+}
+export interface SpecSnapshotHub {
+    name: string;
+    file: string;
+    fanIn: number;
+    covered: boolean;
+}
+export interface SpecSnapshot {
+    version: '1';
+    generatedAt: string;
+    git: {
+        commit: string;
+        branch: string;
+        dirty: boolean;
+    };
+    coverage: {
+        totalFunctions: number;
+        coveredFunctions: number;
+        orphanFunctions: number;
+        coveragePct: number;
+    };
+    domains: SpecSnapshotDomain[];
+    hubs: SpecSnapshotHub[];
+}
+export interface AuditUncoveredFunction {
+    name: string;
+    file: string;
+    kind: string;
+    fanIn: number;
+    fanOut: number;
+    isHub: boolean;
+}
+export interface AuditOrphanRequirement {
+    requirement: string;
+    domain: string;
+    specFile: string;
+}
+export interface AuditStaleDomain {
+    name: string;
+    specFile: string;
+    specModifiedAt: string;
+    sourcesModifiedAt: string;
+    staleSince: string;
+}
+export interface AuditReport {
+    generatedAt: string;
+    summary: {
+        totalFunctions: number;
+        coveredFunctions: number;
+        coveragePct: number;
+        uncoveredCount: number;
+        hubGapCount: number;
+        orphanRequirementCount: number;
+        staleDomainCount: number;
+    };
+    uncoveredFunctions: AuditUncoveredFunction[];
+    hubGaps: AuditUncoveredFunction[];
+    orphanRequirements: AuditOrphanRequirement[];
+    staleDomains: AuditStaleDomain[];
+}
 //# sourceMappingURL=index.d.ts.map

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

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package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "spec-gen-cli",
-  "version": "1.2.5",
+  "version": "1.2.7",
   "description": "Reverse-engineer OpenSpec specifications from existing codebases",
   "type": "module",
   "main": "dist/api/index.js",
@@ -116,5 +116,8 @@
     "typescript": "^5.7.2",
     "typescript-eslint": "^8.19.1",
     "vitest": "^4.0.18"
+  },
+  "optionalDependencies": {
+    "tree-sitter-cli": "^0.23"
   }
 }

package/src/viewer/InteractiveGraphViewer.jsx

@@ -289,10 +289,39 @@ export default function App({ graphUrl, mappingUrl = '/api/mapping', specUrl = '
     return () => window.removeEventListener('keydown', onKey);
   }, [clearSelection]);
 
+  // Track which clusters were auto-expanded by the chatbot (so we can collapse them on clear)
+  const chatExpandedClusters = useRef(new Set());
+  // Track whether selectedId was set by the chatbot (so we can clear it on clear)
+  const chatSelectedId = useRef(null);
+
   // Auto-expand clusters when their nodes are highlighted by the chatbot
   useEffect(() => {
-    if (!graph || focusedIds.length === 0) return;
-    
+    if (!graph) return;
+
+    if (focusedIds.length === 0) {
+      // focusedIds cleared — collapse clusters that were auto-expanded by chat
+      if (chatExpandedClusters.current.size > 0) {
+        const toCollapse = new Set(chatExpandedClusters.current);
+        chatExpandedClusters.current = new Set();
+        setExpandedClusters((prev) => {
+          const next = new Set(prev);
+          toCollapse.forEach((cid) => next.delete(cid));
+          return next;
+        });
+        // If the selected node is inside a collapsing cluster, clear selection
+        // to avoid ghost edges rendering from cluster centers
+        if (selectedId) {
+          const selNode = graph.nodes.find((n) => n.id === selectedId);
+          if (selNode && toCollapse.has(selNode.cluster?.id)) {
+            setSelectedId(null);
+            setAffectedIds([]);
+          }
+        }
+      }
+      chatSelectedId.current = null;
+      return;
+    }
+
     const clusterIdsToExpand = new Set();
     const validNodeIds = [];
     focusedIds.forEach((fid) => {
@@ -302,11 +331,16 @@ export default function App({ graphUrl, mappingUrl = '/api/mapping', specUrl = '
         validNodeIds.push(fid);
       }
     });
-    
+
     if (clusterIdsToExpand.size > 0) {
       setExpandedClusters((prev) => {
         const next = new Set(prev);
-        clusterIdsToExpand.forEach((cid) => next.add(cid));
+        clusterIdsToExpand.forEach((cid) => {
+          if (!prev.has(cid)) {
+            next.add(cid);
+            chatExpandedClusters.current.add(cid);
+          }
+        });
         return next;
       });
     }
@@ -317,6 +351,7 @@ export default function App({ graphUrl, mappingUrl = '/api/mapping', specUrl = '
       setSelectedId(validNodeIds[0]);
       setAffectedIds([]);
       setTab(mapping ? 'spec' : 'node');
+      chatSelectedId.current = validNodeIds[0];
     }
   }, [focusedIds, graph, mapping]);
 
@@ -851,6 +886,13 @@ export default function App({ graphUrl, mappingUrl = '/api/mapping', specUrl = '
             onHighlight={(ids) => setFocusedIds(ids)}
             onHighlightPaths={(paths) => setFocusedPaths(paths)}
             onClose={() => { setChatOpen(false); setFocusedIds([]); setFocusedPaths([]); }}
+            onClearGraph={() => {
+              setFocusedIds([]);
+              setFocusedPaths([]);
+              setExpandedClusters(new Set());
+              setSelectedId(null);
+              setAffectedIds([]);
+            }}
           />
         )}
 

package/src/viewer/components/ChatPanel.jsx

@@ -159,7 +159,7 @@ function ToolSpinner() {
  *   onHighlightPaths(paths: string[])-- called with raw file paths (for class graph)
  *   onClose()                        -- called when the panel is closed
  */
-export function ChatPanel({ onHighlight, onHighlightPaths, onClose }) {
+export function ChatPanel({ onHighlight, onHighlightPaths, onClose, onClearGraph }) {
   const [messages, setMessages] = useState([
     {
       role: 'assistant',
@@ -265,8 +265,7 @@ export function ChatPanel({ onHighlight, onHighlightPaths, onClose }) {
   const clear = () => {
     setMessages([{ role: 'assistant', content: 'Conversation cleared. What would you like to know?' }]);
     setError(null);
-    onHighlight([]);
-    onHighlightPaths?.([]);
+    onClearGraph?.();
   };
 
   return (

package/src/viewer/components/ClusterGraph.jsx

@@ -96,6 +96,25 @@ export function ClusterGraph({
     });
   }, [edges, nodes]);
 
+  // Focused cluster IDs (clusters containing a chat-highlighted node)
+  const focusedClusterIds = useMemo(() => {
+    if (!focusedIds?.length) return null;
+    return new Set(nodes.filter((n) => focusedIds.includes(n.id)).map((n) => n.cluster.id));
+  }, [focusedIds, nodes]);
+
+  // Neighbor cluster IDs (non-focused clusters directly connected to a focused cluster)
+  const neighborClusterIds = useMemo(() => {
+    if (!focusedClusterIds) return null;
+    const neighbors = new Set();
+    clusterEdges.forEach((e) => {
+      if (focusedClusterIds.has(e.source) && !focusedClusterIds.has(e.target))
+        neighbors.add(e.target);
+      if (focusedClusterIds.has(e.target) && !focusedClusterIds.has(e.source))
+        neighbors.add(e.source);
+    });
+    return neighbors;
+  }, [focusedClusterIds, clusterEdges]);
+
   return (
     <svg
       viewBox="0 0 900 540"
@@ -141,9 +160,6 @@ export function ClusterGraph({
         {/* Inter-cluster edges */}
         {!selectedId &&
           (() => {
-            const focusedClusterIds = focusedIds?.length > 0
-              ? new Set(nodes.filter((n) => focusedIds.includes(n.id)).map((n) => n.cluster.id))
-              : null;
             return clusterEdges.map((e) => {
             const s = clusterPos[e.source],
               t = clusterPos[e.target];
@@ -156,10 +172,11 @@ export function ClusterGraph({
             const rs = 38,
               rt = 38;
             const w = Math.min(1 + e.count * 0.15, 4);
+            // dim edge only when BOTH endpoints are non-focused (OR logic)
             const isDimEdge = focusedClusterIds &&
               !focusedClusterIds.has(e.source) && !focusedClusterIds.has(e.target);
             return (
-              <g key={e.id}>
+              <g key={e.id} opacity={isDimEdge ? 0.06 : 0.5}>
                 <line
                   x1={s.x + nx * rs}
                   y1={s.y + ny * rs}
@@ -167,7 +184,6 @@ export function ClusterGraph({
                   y2={t.y - ny * (rt + 5)}
                   stroke="var(--ac-arrow)"
                   strokeWidth={w}
-                  strokeOpacity={isDimEdge ? 0.06 : 0.5}
                   markerEnd="url(#carr)"
                 />
                 <text
@@ -302,7 +318,7 @@ export function ClusterGraph({
                     filter={
                       noGlow ? undefined : isExpanded ? 'url(#cglow)' : isLinkedCollapsed ? 'url(#cglow)' : undefined
                     }
-                    opacity={isClusterGreyed ? 0.18 : 1}
+                    opacity={isClusterGreyed ? (neighborClusterIds?.has(cl.id) ? 0.4 : 0.18) : 1}
                   >
                     <title>{cl.name} — {allMembers.length} file{allMembers.length !== 1 ? 's' : ''}</title>
                     <circle