@ctxo/cli 0.12.0 → 0.13.1

package/README.md

@@ -20,7 +20,7 @@ ctxo index
   <img src="https://img.shields.io/badge/Get%20Started-%E2%86%92-06b6d4?style=for-the-badge&labelColor=0f172a" alt="Get Started →">
 </a>
 
-<sub>Detects your languages, installs the right plugins, wires Ctxo into your AI client, installs git hooks, and builds the first index  one command.</sub>
+<sub>Detects your languages, installs the right plugins, wires Ctxo into your AI client, installs git hooks, and builds the first index, all in one command.</sub>
 
 </div>
 
@@ -28,7 +28,7 @@ ctxo index
 
 ## The Problem: agents code blind
 
-Drop a modern coding agent into a real repo. It ripgreps a symbol, gets 47 hits, reads five files to find the definition, five more for callers  **misses the subclass entirely** (inheritance doesn't show up in text search), **never checks git history** (and confidently reintroduces a bug that was reverted three weeks ago), then runs out of context and starts hallucinating.
+Drop a modern coding agent into a real repo. It ripgreps a symbol, gets 47 hits, reads five files to find the definition, five more for callers, **misses the subclass entirely** (inheritance doesn't show up in text search), **never checks git history** (and confidently reintroduces a bug that was reverted three weeks ago), then runs out of context and starts hallucinating.
 
 It's not a skill gap. It's a **sensory gap**. The agent is navigating your codebase with its eyes closed and a phone book.
 
@@ -36,11 +36,11 @@ It's not a skill gap. It's a **sensory gap**. The agent is navigating your codeb
 
 The core shift: your agent stops reacting to files it stumbles into and starts planning from a complete map. **Blast radius before the edit. Git intent before the bug fix. Importer list before the rename.**
 
-Ctxo indexes your repo once kept fresh by file watchers and git hooks into a deterministic graph: every symbol, every edge (imports, calls, extends, implements), every relevant git commit with intent classified, every anti-pattern. All exposed through 14 semantic MCP tools.
+Ctxo indexes your repo once, kept fresh by file watchers and git hooks, into a deterministic graph: every symbol, every edge (imports, calls, extends, implements, uses, and the data edges reads, writes and executes), every relevant git commit with intent classified, every anti-pattern. All exposed through 14 semantic MCP tools.
 
 One `get_blast_radius` call replaces an entire ripgrep/read spiral. One `get_pr_impact` replaces a full review session of "wait, what calls this?"
 
-The agent still writes the code. It just stops writing it **blind** so the bug never has to be caught by the compiler, the tests, CI, or a user.
+The agent still writes the code. It just stops writing it **blind**, so the bug never has to be caught by the compiler, the tests, CI, or a user.
 
 ## Codebase Dashboard
 
@@ -71,6 +71,26 @@ The safe-edit guard closes this loop deterministically. When you run `ctxo init`
 
 If an agent tries to edit a high-impact symbol without first calling `get_blast_radius`, the hook blocks the edit and tells the agent what to check. Once the agent runs the tool, the edit goes through normally. Fires once per symbol per session, fail-open on any uncertainty.
 
+With the hook and the skills doing the work, the always-loaded `CLAUDE.md` block shrinks to four lines:
+
+```markdown
+## ctxo
+
+This repo has a ctxo index: dependency graph, git intent, change health. For structural questions (who depends on X, what breaks if X changes, why X looks like this), use the ctxo MCP tools before grepping.
+A pre-edit guard blocks the first edit to a high-impact symbol until `get_blast_radius` has been called for it.
+Skills: `ctxo-understand` (orient at task start), `ctxo-safe-edit` (before changing a symbol), `ctxo-review-pr` (before reviewing a diff).
+```
+
+Every other client, Claude Code without the guard, and a `CLAUDE.md` that another client reads too (an `AGENTS.md` linked to it) get the full tool guide. Re-running `ctxo init` replaces the block in place and keeps the rest of your file. The blocks and skills are written in Prettier's layout and compared with formatting ignored, so a markdown formatter and ctxo never rewrite each other. `ctxo doctor` warns when the block, the skills or the hook drift, and `ctxo doctor --fix` repairs them.
+
+**Pick the parts:**
+
+```shell
+ctxo init --only rules,skills,guard   # add the guard and the skills; the rules block follows
+ctxo init --skip git-hooks            # everything except the git hooks
+ctxo init --no-guard                  # does not install the guard (CLAUDE.md gets the full block unless a guard is already registered)
+```
+
 **Tune it:**
 
 ```shell
@@ -97,19 +117,45 @@ gate:
 | Cursor | no (no blocking pre-edit hook) | yes | yes |
 | Other | no | where supported | yes |
 
+## Fresh on every commit
+
+A stale index is worse than none: the agent trusts a map that no longer matches the code. `ctxo init` installs a post-commit hook that runs `ctxo index --commit HEAD` once per commit. It re-indexes only the files that commit changed, refreshes the co-change matrix from git history, and records one snapshot per commit for the drift and boundary signals.
+
+```shell
+ctxo index --commit HEAD                                 # what the hook runs
+ctxo index --files src/a.ts src/b.ts                     # re-index a few files
+ctxo index --cochange-commits 500 --cochange-since 12m   # co-change window (or `cochange:` in config.yaml)
+ctxo doctor --fix                                        # upgrades an old hook block in place
+```
+
+The file you forget to touch is usually the one no import points at. Files that keep changing together are coupled anyway: `get_blast_radius` promotes a dependent that co-changes with your target from `potential` to `likely`, and lists the files with no dependency path at all as `coChangedFiles`. `ctxo index --max-history` only controls how many commits each file keeps for `get_why_context`; the co-change window has its own settings.
+
+## Where the boundaries really are
+
+Folder names say one thing; imports and commit history often say another. `ctxo index` also writes candidate bounded contexts: files clustered by dependency and co-change edges, with hub files damped, each with a suggested label, a cohesion score, top terms and the edges that cross into other candidates. With `@ctxo/lang-sql` installed, tables, views and procedures join the graph: a table's readers and writers show up in its blast radius, and each candidate lists the tables it shares with other candidates.
+
+```shell
+ctxo contexts          # candidates as a table
+ctxo contexts --json   # the full contexts-view.json
+```
+
+Agents get the same view from `get_architectural_overlay(mode: "contexts")`, and one candidate in full with `candidate: <id>`.
+
 ## Supported Languages
 
 | Language | Plugin | Tier | Notes |
 |---|---|---|---|
-| TypeScript / JavaScript | `@ctxo/lang-typescript` | full | ts-morph; type-aware cross-file resolution |
-| Go | `@ctxo/lang-go` | syntax | tree-sitter; exported-symbol analysis |
+| TypeScript / JavaScript | `@ctxo/lang-typescript` | full | ts-morph; type-aware cross-file resolution; decorators as annotations; test blocks as symbols; SQL at known call sites (pg, mysql2, mssql, knex, Prisma, TypeORM, Sequelize, better-sqlite3 raw SQL) |
+| Go | `@ctxo/lang-go` | syntax / full | `ctxo-go-analyzer` full tier (Go 1.22+), tree-sitter fallback; struct tags as annotations; `_test.go` functions as symbols (full tier); SQL at known call sites (`database/sql`, sqlx, pgx, gorm raw; full tier) |
 | C# | `@ctxo/lang-csharp` | full | Roslyn; .NET SDK 8+ for full tier, tree-sitter fallback |
-| Java | `@ctxo/lang-java` | syntax / full | tree-sitter syntax tier built-in; full tier via `@ctxo/lang-java-analyzer` companion (JRE 11+ required, covers Java 8-21); detected by `pom.xml` / `build.gradle` |
+| Java | `@ctxo/lang-java` | syntax / full | tree-sitter syntax tier built-in; full tier via `@ctxo/lang-java-analyzer` companion (JRE 11+ required, covers Java 8-21); detected by `pom.xml` / `build.gradle`; annotations in both tiers; test methods with their annotations; SQL at known call sites (JDBC, Spring `JdbcTemplate`, JPA native queries, MyBatis; full tier) |
+| SQL (T-SQL) | `@ctxo/lang-sql` | syntax | `.sql` tables, views, procedures and functions with `reads` / `writes` / `executes` edges; no database or .NET needed. With it installed, the C# plugin's Roslyn tier also links constant SQL at ADO.NET, Dapper, `SqlBulkCopy` and EF Core call sites to the same tables, and so do the TypeScript, Java and Go plugins at their known call sites |
 
 Install via the CLI shortcut:
 
 ```bash
 ctxo install typescript go csharp   # syntax or full tier auto-detected
+ctxo install sql                    # T-SQL plugin (alias tsql)
 ctxo install java                   # installs syntax tier; adds full-tier analyzer when JRE 11+ detected
 ctxo install java --full-tier       # force full-tier analyzer install
 ctxo install java --syntax-only     # skip analyzer, syntax tier only
@@ -117,7 +163,7 @@ ctxo install java --syntax-only     # skip analyzer, syntax tier only
 
 ## Links
 
-* [Docs](https://alperhankendi.github.io/Ctxo/docs/)  quick start, MCP tools, CLI reference, integrations
+* [Docs](https://alperhankendi.github.io/Ctxo/docs/): quick start, MCP tools, CLI reference, integrations
 * [npm](https://www.npmjs.com/package/@ctxo/cli)
 * [Changelog](CHANGELOG.md)
 * [LLM Reference](llms-full.txt)

package/dist/{chunk-CDGQGCVN.js → chunk-DT3ZH4AU.js}

@@ -9,22 +9,8 @@ import { join, relative } from "path";
 
 // src/core/types.ts
 import { z } from "zod";
-var SYMBOL_KINDS = [
-  "function",
-  "class",
-  "interface",
-  "method",
-  "variable",
-  "type"
-];
+import { SYMBOL_KINDS, EDGE_KINDS, FACT_KINDS } from "@ctxo/plugin-api";
 var SymbolKindSchema = z.enum(SYMBOL_KINDS);
-var EDGE_KINDS = [
-  "imports",
-  "calls",
-  "extends",
-  "implements",
-  "uses"
-];
 var EdgeKindSchema = z.enum(EDGE_KINDS);
 var DetailLevelSchema = z.union([
   z.literal(1),
@@ -52,6 +38,11 @@ var EdgeTargetSchema = z.string().refine(
   },
   { message: "edge target must be <file>::<name>::<kind> or <name>::<kind>" }
 );
+var SymbolAnnotationSchema = z.object({
+  name: z.string().min(1),
+  args: z.array(z.string()).readonly().optional(),
+  named: z.record(z.string(), z.string()).readonly().optional()
+});
 var SymbolNodeSchema = z.object({
   symbolId: SymbolIdSchema,
   name: z.string().min(1),
@@ -59,7 +50,8 @@ var SymbolNodeSchema = z.object({
   startLine: z.number().int().nonnegative(),
   endLine: z.number().int().nonnegative(),
   startOffset: z.number().int().nonnegative().optional(),
-  endOffset: z.number().int().nonnegative().optional()
+  endOffset: z.number().int().nonnegative().optional(),
+  annotations: z.array(SymbolAnnotationSchema).readonly().optional()
 }).refine((node) => node.endLine >= node.startLine, {
   message: "endLine must be >= startLine"
 });
@@ -82,6 +74,14 @@ var AntiPatternSchema = z.object({
   message: z.string(),
   date: z.string().min(1)
 });
+var FactKindSchema = z.enum(FACT_KINDS);
+var CodeFactSchema = z.object({
+  kind: FactKindSchema,
+  symbolId: SymbolIdSchema,
+  line: z.number().int().nonnegative(),
+  text: z.string(),
+  detail: z.record(z.string(), z.string()).readonly().optional()
+});
 var ComplexityMetricsSchema = z.object({
   symbolId: z.string().min(1),
   cyclomatic: z.number().nonnegative()
@@ -94,17 +94,56 @@ var FileIndexSchema = z.object({
   edges: z.array(GraphEdgeSchema),
   complexity: z.array(ComplexityMetricsSchema).optional(),
   intent: z.array(CommitIntentSchema),
-  antiPatterns: z.array(AntiPatternSchema)
+  antiPatterns: z.array(AntiPatternSchema),
+  facts: z.array(CodeFactSchema).readonly().optional()
+});
+var CoChangeEntrySchema = z.object({
+  file1: z.string().min(1),
+  file2: z.string().min(1),
+  sharedCommits: z.number().int().min(1),
+  frequency: z.number().min(0).max(1)
+});
+var CoChangeWindowMetaSchema = z.object({
+  maxCommits: z.union([z.number().int().min(1), z.literal("all")]),
+  since: z.string().optional(),
+  head: z.string().min(1),
+  commitsScanned: z.number().int().min(0),
+  commitsUsed: z.number().int().min(0),
+  massSkipped: z.number().int().min(0),
+  maxFilesPerCommit: z.number().int().min(1),
+  minShared: z.number().int().min(1)
+});
+var CoChangeMatrixSchema = z.object({
+  version: z.literal(1),
+  timestamp: z.number(),
+  window: CoChangeWindowMetaSchema.optional(),
+  entries: z.array(CoChangeEntrySchema)
 });
 
 // src/adapters/storage/json-index-reader.ts
 var log = createLogger("ctxo:json-reader");
+var INDEX_ARTIFACT_FILES = [
+  "co-changes.json",
+  "communities.json",
+  "drift-events.json",
+  "boundary-violations.json",
+  "contexts-view.json"
+];
+var COMMUNITY_HISTORY_DIR = "communities.history";
 var JsonIndexReader = class {
   indexDir;
   constructor(ctxoRoot) {
     this.indexDir = join(ctxoRoot, "index");
   }
   readAll() {
+    return this.readEntries().map((entry) => entry.index);
+  }
+  /**
+   * Every valid index entry together with the path of the JSON file it came from. A caller that wants to
+   * delete an entry must use this path: the `file` field inside the JSON says which source file the entry
+   * is for, but a corrupt or crafted file can claim any name, such as an artifact's.
+   */
+  readEntries() {
     if (!existsSync(this.indexDir)) {
       return [];
     }
@@ -113,7 +152,7 @@ var JsonIndexReader = class {
     for (const filePath of jsonFiles) {
       const parsed = this.readSingle(filePath);
       if (parsed) {
-        results.push(parsed);
+        results.push({ path: filePath, index: parsed });
       }
     }
     return results;
@@ -138,17 +177,35 @@ var JsonIndexReader = class {
       const rawEdges = Array.isArray(raw_data["edges"]) ? raw_data["edges"] : [];
       const rawIntent = Array.isArray(raw_data["intent"]) ? raw_data["intent"] : [];
       const rawAntiPatterns = Array.isArray(raw_data["antiPatterns"]) ? raw_data["antiPatterns"] : [];
-      const validSymbols = rawSymbols.filter((s) => SymbolNodeSchema.safeParse(s).success);
+      let droppedAnnotations = 0;
+      const validSymbols = [];
+      for (const sym of rawSymbols) {
+        if (SymbolNodeSchema.safeParse(sym).success) {
+          validSymbols.push(sym);
+          continue;
+        }
+        if (sym !== null && typeof sym === "object" && "annotations" in sym) {
+          const { annotations: _dropped, ...withoutAnnotations } = sym;
+          if (SymbolNodeSchema.safeParse(withoutAnnotations).success) {
+            validSymbols.push(withoutAnnotations);
+            droppedAnnotations++;
+          }
+        }
+      }
+      const factsPresent = raw_data["facts"] !== void 0;
+      const rawFacts = Array.isArray(raw_data["facts"]) ? raw_data["facts"] : void 0;
+      const validFacts = rawFacts?.filter((f) => CodeFactSchema.safeParse(f).success);
       const validEdges = rawEdges.filter((e) => GraphEdgeSchema.safeParse(e).success);
       const validIntent = rawIntent.filter((i) => CommitIntentSchema.safeParse(i).success);
       const validAntiPatterns = rawAntiPatterns.filter((a) => AntiPatternSchema.safeParse(a).success);
       const droppedSymbols = rawSymbols.length - validSymbols.length;
+      const droppedFacts = rawFacts && validFacts ? rawFacts.length - validFacts.length : factsPresent ? 1 : 0;
       const droppedEdges = rawEdges.length - validEdges.length;
       const droppedIntent = rawIntent.length - validIntent.length;
       const droppedAntiPatterns = rawAntiPatterns.length - validAntiPatterns.length;
-      if (droppedSymbols > 0 || droppedEdges > 0 || droppedIntent > 0 || droppedAntiPatterns > 0) {
+      if (droppedSymbols > 0 || droppedEdges > 0 || droppedIntent > 0 || droppedAntiPatterns > 0 || droppedAnnotations > 0 || droppedFacts > 0) {
         log.warn(
-          `${rel}: dropped ${droppedSymbols} invalid symbol(s), ${droppedEdges} invalid edge(s), ${droppedIntent} invalid intent(s), ${droppedAntiPatterns} invalid antiPattern(s) \u2014 kept ${validSymbols.length} symbol(s), ${validEdges.length} edge(s), ${validIntent.length} intent(s), ${validAntiPatterns.length} antiPattern(s)`
+          `${rel}: dropped ${droppedSymbols} invalid symbol(s), ${droppedEdges} invalid edge(s), ${droppedIntent} invalid intent(s), ${droppedAntiPatterns} invalid antiPattern(s), ${droppedAnnotations} invalid annotation list(s), ${droppedFacts} invalid fact(s); kept ${validSymbols.length} symbol(s), ${validEdges.length} edge(s), ${validIntent.length} intent(s), ${validAntiPatterns.length} antiPattern(s)`
         );
       }
       const recovered = FileIndexSchema.safeParse({
@@ -156,7 +213,8 @@ var JsonIndexReader = class {
         symbols: validSymbols,
         edges: validEdges,
         intent: validIntent,
-        antiPatterns: validAntiPatterns
+        antiPatterns: validAntiPatterns,
+        facts: validFacts
       });
       if (!recovered.success) {
         console.error(
@@ -182,9 +240,9 @@ var JsonIndexReader = class {
       if (entry.isSymbolicLink()) continue;
       const fullPath = join(dir, entry.name);
       if (entry.isDirectory()) {
-        if (entry.name === "communities.history") continue;
+        if (entry.name === COMMUNITY_HISTORY_DIR) continue;
         files.push(...this.collectJsonFiles(fullPath, visited));
-      } else if (entry.name.endsWith(".json") && entry.name !== "co-changes.json" && entry.name !== "communities.json" && entry.name !== "drift-events.json" && entry.name !== "boundary-violations.json") {
+      } else if (entry.name.endsWith(".json") && !INDEX_ARTIFACT_FILES.includes(entry.name)) {
         files.push(fullPath);
       }
     }
@@ -193,7 +251,14 @@ var JsonIndexReader = class {
 };
 
 export {
+  SYMBOL_KINDS,
+  EDGE_KINDS,
+  SymbolKindSchema,
+  EdgeKindSchema,
   DetailLevelSchema,
+  CoChangeMatrixSchema,
+  INDEX_ARTIFACT_FILES,
+  COMMUNITY_HISTORY_DIR,
   JsonIndexReader
 };
-//# sourceMappingURL=chunk-CDGQGCVN.js.map
+//# sourceMappingURL=chunk-DT3ZH4AU.js.map

package/dist/chunk-DT3ZH4AU.js.map

@@ -0,0 +1 @@
+{"version":3,"sources":["../src/adapters/storage/json-index-reader.ts","../src/core/types.ts"],"sourcesContent":["import { readFileSync, readdirSync, existsSync, realpathSync } from 'node:fs';\nimport { join, relative } from 'node:path';\nimport {\n  FileIndexSchema,\n  SymbolNodeSchema,\n  GraphEdgeSchema,\n  CommitIntentSchema,\n  AntiPatternSchema,\n  CodeFactSchema,\n  type FileIndex,\n} from '../../core/types.js';\nimport { createLogger } from '../../core/logger.js';\n\nconst log = createLogger('ctxo:json-reader');\n\n/** JSON files next to the index entries that are products of Ctxo, not entries: the reader skips them. */\nexport const INDEX_ARTIFACT_FILES: readonly string[] = [\n  'co-changes.json',\n  'communities.json',\n  'drift-events.json',\n  'boundary-violations.json',\n  'contexts-view.json',\n];\n\n/** The folder of archived community snapshots inside the index folder: not entries either. */\nexport const COMMUNITY_HISTORY_DIR = 'communities.history';\n\n/** One index entry and the JSON file on disk it was read from. */\nexport interface IndexEntry {\n  readonly path: string;\n  readonly index: FileIndex;\n}\n\nexport class JsonIndexReader {\n  private readonly indexDir: string;\n\n  constructor(ctxoRoot: string) {\n    this.indexDir = join(ctxoRoot, 'index');\n  }\n\n  readAll(): FileIndex[] {\n    return this.readEntries().map((entry) => entry.index);\n  }\n\n  /**\n   * Every valid index entry together with the path of the JSON file it came from. A caller that wants to\n   * delete an entry must use this path: the `file` field inside the JSON says which source file the entry\n   * is for, but a corrupt or crafted file can claim any name, such as an artifact's.\n   */\n  readEntries(): IndexEntry[] {\n    if (!existsSync(this.indexDir)) {\n      return [];\n    }\n\n    const jsonFiles = this.collectJsonFiles(this.indexDir);\n    const results: IndexEntry[] = [];\n\n    for (const filePath of jsonFiles) {\n      const parsed = this.readSingle(filePath);\n      if (parsed) {\n        results.push({ path: filePath, index: parsed });\n      }\n    }\n\n    return results;\n  }\n\n  readSingle(absolutePath: string): FileIndex | undefined {\n    try {\n      const raw = readFileSync(absolutePath, 'utf-8');\n      const data: unknown = JSON.parse(raw);\n      const result = FileIndexSchema.safeParse(data);\n\n      if (result.success) {\n        return result.data;\n      }\n\n      // Strict parse failed — attempt resilient recovery: keep valid items, drop invalid ones.\n      const rel = relative(this.indexDir, absolutePath);\n      const raw_data = data as Record<string, unknown>;\n\n      // Must have at least a valid file name and lastModified to be recoverable.\n      if (typeof raw_data['file'] !== 'string' || !raw_data['file'] ||\n          typeof raw_data['lastModified'] !== 'number') {\n        console.error(\n          `[ctxo:json-reader] Invalid schema in ${rel}: ${result.error.message}`,\n        );\n        return undefined;\n      }\n\n      const rawSymbols = Array.isArray(raw_data['symbols']) ? raw_data['symbols'] : [];\n      const rawEdges = Array.isArray(raw_data['edges']) ? raw_data['edges'] : [];\n      const rawIntent = Array.isArray(raw_data['intent']) ? raw_data['intent'] : [];\n      const rawAntiPatterns = Array.isArray(raw_data['antiPatterns']) ? raw_data['antiPatterns'] : [];\n\n      // A symbol that fails only because of its annotations is kept without them: annotations are\n      // optional metadata and must not cost the symbol.\n      let droppedAnnotations = 0;\n      const validSymbols: unknown[] = [];\n      for (const sym of rawSymbols) {\n        if (SymbolNodeSchema.safeParse(sym).success) {\n          validSymbols.push(sym);\n          continue;\n        }\n        if (sym !== null && typeof sym === 'object' && 'annotations' in sym) {\n          const { annotations: _dropped, ...withoutAnnotations } = sym as Record<string, unknown>;\n          if (SymbolNodeSchema.safeParse(withoutAnnotations).success) {\n            validSymbols.push(withoutAnnotations);\n            droppedAnnotations++;\n          }\n        }\n      }\n      // A facts value that is present but not an array is treated as absent: facts are optional metadata\n      // and must not cost the file. It counts as one dropped fact list in the warning.\n      const factsPresent = raw_data['facts'] !== undefined;\n      const rawFacts = Array.isArray(raw_data['facts']) ? raw_data['facts'] : undefined;\n      const validFacts = rawFacts?.filter((f) => CodeFactSchema.safeParse(f).success);\n      const validEdges = rawEdges.filter((e) => GraphEdgeSchema.safeParse(e).success);\n      const validIntent = rawIntent.filter((i) => CommitIntentSchema.safeParse(i).success);\n      const validAntiPatterns = rawAntiPatterns.filter((a) => AntiPatternSchema.safeParse(a).success);\n\n      const droppedSymbols = rawSymbols.length - validSymbols.length;\n      const droppedFacts = rawFacts && validFacts\n        ? rawFacts.length - validFacts.length\n        : factsPresent ? 1 : 0;\n      const droppedEdges = rawEdges.length - validEdges.length;\n      const droppedIntent = rawIntent.length - validIntent.length;\n      const droppedAntiPatterns = rawAntiPatterns.length - validAntiPatterns.length;\n\n      if (droppedSymbols > 0 || droppedEdges > 0 || droppedIntent > 0 || droppedAntiPatterns > 0 ||\n          droppedAnnotations > 0 || droppedFacts > 0) {\n        log.warn(\n          `${rel}: dropped ${droppedSymbols} invalid symbol(s), ${droppedEdges} invalid edge(s), ${droppedIntent} invalid intent(s), ${droppedAntiPatterns} invalid antiPattern(s), ${droppedAnnotations} invalid annotation list(s), ${droppedFacts} invalid fact(s); kept ${validSymbols.length} symbol(s), ${validEdges.length} edge(s), ${validIntent.length} intent(s), ${validAntiPatterns.length} antiPattern(s)`,\n        );\n      }\n\n      // Re-parse with the filtered arrays to get a fully-typed FileIndex.\n      const recovered = FileIndexSchema.safeParse({\n        ...raw_data,\n        symbols: validSymbols,\n        edges: validEdges,\n        intent: validIntent,\n        antiPatterns: validAntiPatterns,\n        facts: validFacts,\n      });\n\n      if (!recovered.success) {\n        console.error(\n          `[ctxo:json-reader] Invalid schema in ${rel}: ${result.error.message}`,\n        );\n        return undefined;\n      }\n\n      return recovered.data;\n    } catch (err) {\n      const rel = relative(this.indexDir, absolutePath);\n      console.error(\n        `[ctxo:json-reader] Failed to read ${rel}: ${(err as Error).message}`,\n      );\n      return undefined;\n    }\n  }\n\n  private collectJsonFiles(dir: string, visited: Set<string> = new Set()): string[] {\n    const realDir = realpathSync(dir);\n    if (visited.has(realDir)) return []; // Guard against symlink loops\n    visited.add(realDir);\n\n    const files: string[] = [];\n\n    for (const entry of readdirSync(dir, { withFileTypes: true })) {\n      if (entry.isSymbolicLink()) continue; // Skip symlinks entirely\n\n      const fullPath = join(dir, entry.name);\n      if (entry.isDirectory()) {\n        // Skip non-FileIndex directories under .ctxo/index/\n        if (entry.name === COMMUNITY_HISTORY_DIR) continue;\n        files.push(...this.collectJsonFiles(fullPath, visited));\n      } else if (entry.name.endsWith('.json') && !INDEX_ARTIFACT_FILES.includes(entry.name)) {\n        files.push(fullPath);\n      }\n    }\n\n    return files;\n  }\n}\n","import { z } from 'zod';\nimport { SYMBOL_KINDS, EDGE_KINDS, FACT_KINDS } from '@ctxo/plugin-api';\n\n// ── Symbol Kinds ────────────────────────────────────────────────\n\nexport { SYMBOL_KINDS };\n\nexport const SymbolKindSchema = z.enum(SYMBOL_KINDS);\nexport type SymbolKind = z.infer<typeof SymbolKindSchema>;\n\n// ── Edge Kinds ──────────────────────────────────────────────────\n\nexport { EDGE_KINDS };\n\nexport const EdgeKindSchema = z.enum(EDGE_KINDS);\nexport type EdgeKind = z.infer<typeof EdgeKindSchema>;\n\n// ── Detail Levels ───────────────────────────────────────────────\n\nexport const DETAIL_LEVELS = [1, 2, 3, 4] as const;\n\nexport const DetailLevelSchema = z.union([\n  z.literal(1),\n  z.literal(2),\n  z.literal(3),\n  z.literal(4),\n]);\nexport type DetailLevel = z.infer<typeof DetailLevelSchema>;\n\n// ── Symbol ID ───────────────────────────────────────────────────\n\n/**\n * Format: \"<relativeFile>::<name>::<kind>\"\n * Example: \"src/foo.ts::myFn::function\"\n */\nexport const SymbolIdSchema = z\n  .string()\n  .min(1)\n  .refine(\n    (value) => {\n      const parts = value.split('::');\n      if (parts.length !== 3) return false;\n      const [file, name, kind] = parts;\n      if (!file || !name || !kind) return false;\n      return SymbolKindSchema.safeParse(kind).success;\n    },\n    { message: 'Symbol ID must match format \"<file>::<name>::<kind>\"' },\n  );\nexport type SymbolId = z.infer<typeof SymbolIdSchema>;\n\n// ── Edge Target ─────────────────────────────────────────────────\n\n/**\n * An edge target: either a full 3-part symbol ID (\"<file>::<name>::<kind>\")\n * or a 2-part name-reference (\"<name>::<kind>\") for cross-file / unresolved\n * targets. The graph builder resolves name-references by name at query time.\n */\nexport const EdgeTargetSchema = z.string().refine(\n  (s) => {\n    const parts = s.split('::');\n    if (parts.length !== 3 && parts.length !== 2) return false;\n    if (parts.some((p) => p.length === 0)) return false;\n    const kind = parts[parts.length - 1];\n    return (SYMBOL_KINDS as readonly string[]).includes(kind as string);\n  },\n  { message: 'edge target must be <file>::<name>::<kind> or <name>::<kind>' },\n);\nexport type EdgeTarget = z.infer<typeof EdgeTargetSchema>;\n\n// ── Symbol Annotation ───────────────────────────────────────────\n\n/** Host-language attribute or decorator on a symbol (protocol v2). Shape only; plugins enforce caps. */\nexport const SymbolAnnotationSchema = z.object({\n  name: z.string().min(1),\n  args: z.array(z.string()).readonly().optional(),\n  named: z.record(z.string(), z.string()).readonly().optional(),\n});\nexport type SymbolAnnotation = z.infer<typeof SymbolAnnotationSchema>;\n\n// ── Symbol Node ─────────────────────────────────────────────────\n\nexport const SymbolNodeSchema = z\n  .object({\n    symbolId: SymbolIdSchema,\n    name: z.string().min(1),\n    kind: SymbolKindSchema,\n    startLine: z.number().int().nonnegative(),\n    endLine: z.number().int().nonnegative(),\n    startOffset: z.number().int().nonnegative().optional(),\n    endOffset: z.number().int().nonnegative().optional(),\n    annotations: z.array(SymbolAnnotationSchema).readonly().optional(),\n  })\n  .refine((node) => node.endLine >= node.startLine, {\n    message: 'endLine must be >= startLine',\n  });\nexport type SymbolNode = z.infer<typeof SymbolNodeSchema>;\n\n// ── Graph Edge ──────────────────────────────────────────────────\n\nexport const GraphEdgeSchema = z.object({\n  from: SymbolIdSchema,    // strict 3-part: from is always a local, resolved symbol\n  to: EdgeTargetSchema,    // 3-part OR 2-part name-ref for cross-file/unresolved targets\n  kind: EdgeKindSchema,\n  typeOnly: z.boolean().optional(),\n});\nexport type GraphEdge = z.infer<typeof GraphEdgeSchema>;\n\n// ── Commit Intent ───────────────────────────────────────────────\n\nexport const CommitIntentSchema = z.object({\n  hash: z.string().min(1),\n  message: z.string(),\n  date: z.string().min(1),\n  kind: z.literal('commit'),\n});\nexport type CommitIntent = z.infer<typeof CommitIntentSchema>;\n\n// ── Anti-Pattern ────────────────────────────────────────────────\n\nexport const AntiPatternSchema = z.object({\n  hash: z.string().min(1),\n  message: z.string(),\n  date: z.string().min(1),\n});\nexport type AntiPattern = z.infer<typeof AntiPatternSchema>;\n\n// ── Code Fact ───────────────────────────────────────────────────\n\nexport const FactKindSchema = z.enum(FACT_KINDS);\nexport type FactKind = z.infer<typeof FactKindSchema>;\n\n/** A fact extracted from a symbol body (protocol v2). The line is 0-based, like a symbol's start line. */\nexport const CodeFactSchema = z.object({\n  kind: FactKindSchema,\n  symbolId: SymbolIdSchema,\n  line: z.number().int().nonnegative(),\n  text: z.string(),\n  detail: z.record(z.string(), z.string()).readonly().optional(),\n});\nexport type CodeFact = z.infer<typeof CodeFactSchema>;\n\n// ── File Index ──────────────────────────────────────────────────\n\nexport const ComplexityMetricsSchema = z.object({\n  symbolId: z.string().min(1),\n  cyclomatic: z.number().nonnegative(),\n});\n\nexport const FileIndexSchema = z.object({\n  file: z.string().min(1),\n  lastModified: z.number().nonnegative(),\n  contentHash: z.string().optional(),\n  symbols: z.array(SymbolNodeSchema),\n  edges: z.array(GraphEdgeSchema),\n  complexity: z.array(ComplexityMetricsSchema).optional(),\n  intent: z.array(CommitIntentSchema),\n  antiPatterns: z.array(AntiPatternSchema),\n  facts: z.array(CodeFactSchema).readonly().optional(),\n});\nexport type FileIndex = z.infer<typeof FileIndexSchema>;\n\n// ── Logic-Slice Result ──────────────────────────────────────────\n\nexport interface LogicSliceResult {\n  readonly root: SymbolNode;\n  readonly dependencies: readonly SymbolNode[];\n  readonly edges: readonly GraphEdge[];\n}\n\n// ── Formatted Slice ─────────────────────────────────────────────\n\nexport interface TruncationInfo {\n  readonly truncated: true;\n  readonly reason: 'token_budget_exceeded';\n}\n\nexport interface FormattedSlice {\n  readonly root: SymbolNode;\n  readonly dependencies: readonly SymbolNode[];\n  readonly edges: readonly GraphEdge[];\n  readonly level: DetailLevel;\n  readonly levelDescription?: string;\n  readonly truncation?: TruncationInfo;\n}\n\n// ── Complexity & Churn ──────────────────────────────────────────\n\nexport interface ComplexityMetrics {\n  readonly symbolId: string;\n  readonly cyclomatic: number;\n}\n\nexport interface ChurnData {\n  readonly filePath: string;\n  readonly commitCount: number;\n}\n\nexport const SCORE_BANDS = ['low', 'medium', 'high'] as const;\nexport type ScoreBand = (typeof SCORE_BANDS)[number];\n\nexport interface ChangeIntelligenceScore {\n  readonly symbolId: string;\n  readonly complexity: number;\n  readonly churn: number;\n  readonly composite: number;\n  readonly band: ScoreBand;\n}\n\n// ── Why-Context Result ──────────────────────────────────────────\n\nexport interface WhyContextResult {\n  readonly commitHistory: readonly CommitIntent[];\n  readonly antiPatternWarnings: readonly AntiPattern[];\n  readonly changeIntelligence?: ChangeIntelligenceScore;\n}\n\n// ── Co-Change Analysis ─────────────────────────────────────────\n\nexport interface CoChangeEntry {\n  readonly file1: string;\n  readonly file2: string;\n  readonly sharedCommits: number;\n  readonly frequency: number;\n}\n\n/** The window a co-change matrix was built from and the filters that shaped it. */\nexport interface CoChangeWindowMeta {\n  /** Configured commit limit: the last N non-merge commits from HEAD, or 'all'. */\n  readonly maxCommits: number | 'all';\n  /** Configured duration limit such as \"12m\", anchored to HEAD's committer date. */\n  readonly since?: string;\n  /** Short SHA of HEAD when the matrix was built. */\n  readonly head: string;\n  /** Commits inside the window. */\n  readonly commitsScanned: number;\n  /** Window commits that fed the counts. */\n  readonly commitsUsed: number;\n  /** Window commits skipped for touching more than `maxFilesPerCommit` included files. */\n  readonly massSkipped: number;\n  readonly maxFilesPerCommit: number;\n  readonly minShared: number;\n}\n\nexport interface CoChangeMatrix {\n  readonly version: 1;\n  readonly timestamp: number;\n  /** Absent in matrices written before the window was recorded. */\n  readonly window?: CoChangeWindowMeta;\n  readonly entries: readonly CoChangeEntry[];\n}\n\nconst CoChangeEntrySchema = z.object({\n  file1: z.string().min(1),\n  file2: z.string().min(1),\n  sharedCommits: z.number().int().min(1),\n  frequency: z.number().min(0).max(1),\n});\n\nconst CoChangeWindowMetaSchema = z.object({\n  maxCommits: z.union([z.number().int().min(1), z.literal('all')]),\n  since: z.string().optional(),\n  head: z.string().min(1),\n  commitsScanned: z.number().int().min(0),\n  commitsUsed: z.number().int().min(0),\n  massSkipped: z.number().int().min(0),\n  maxFilesPerCommit: z.number().int().min(1),\n  minShared: z.number().int().min(1),\n});\n\n/**\n * Validates `co-changes.json`. `entries` is required and `window` optional, so files written before\n * the window was recorded still load. Unknown keys are dropped rather than rejected, so a file from\n * a newer Ctxo stays readable.\n */\nexport const CoChangeMatrixSchema: z.ZodType<CoChangeMatrix> = z.object({\n  version: z.literal(1),\n  timestamp: z.number(),\n  window: CoChangeWindowMetaSchema.optional(),\n  entries: z.array(CoChangeEntrySchema),\n});\n\n// ── Commit Record (from git adapter) ────────────────────────────\n\nexport interface CommitRecord {\n  readonly hash: string;\n  readonly message: string;\n  readonly date: string;\n  readonly author: string;\n}\n\n// ── Change Log (from git adapter) ───────────────────────────────\n\n/** git name-status letters Ctxo keeps; A added, M modified, D deleted, R renamed, C copied, T type changed. */\nexport type FileChangeStatus = 'A' | 'M' | 'D' | 'R' | 'C' | 'T';\n\nexport interface FileChange {\n  readonly status: FileChangeStatus;\n  /** Path after the change: repo-relative, forward slashes. */\n  readonly path: string;\n  /** Path before the change; set only for renames (R) and copies (C). */\n  readonly oldPath?: string;\n}\n\n/** One non-merge commit and the files it changed. */\nexport interface CommitChangeSet {\n  /** Full commit SHA (git %H). */\n  readonly hash: string;\n  /** Subject line (git %s). */\n  readonly message: string;\n  /** Author date, strict ISO 8601 (git %aI). */\n  readonly date: string;\n  /** Author name (git %an). */\n  readonly author: string;\n  /** Committer date in unix seconds (git %ct). */\n  readonly committedAt: number;\n  readonly changes: readonly FileChange[];\n}\n\nexport interface ChangeLog {\n  /** Short SHA of HEAD (git %h), which may itself be a merge commit. */\n  readonly head: string;\n  /** Committer date of HEAD in unix seconds (git %ct). */\n  readonly headCommittedAt: number;\n  /** Non-merge commits reachable from HEAD, newest first. */\n  readonly commits: readonly CommitChangeSet[];\n}\n\n// ── Blame Line (from git adapter) ───────────────────────────────\n\nexport interface BlameLine {\n  readonly hash: string;\n  readonly lineNumber: number;\n  readonly author: string;\n  readonly date: string;\n}\n\n// ── Search Types ───────────────────────────────────────────────\n\nexport interface SearchResult {\n  symbolId: string;\n  name: string;\n  kind: string;\n  filePath: string;\n  /** BM25 relevance score (higher = more relevant) */\n  relevanceScore: number;\n  /** PageRank importance score (0-1) */\n  importanceScore: number;\n  /** Final combined score after all boosts */\n  combinedScore: number;\n}\n\nexport interface SearchMetrics {\n  porterHits: number;\n  trigramHits: number;\n  phase2Activated: boolean;\n  fuzzyApplied: boolean;\n  latencyMs: number;\n}\n\nexport interface FuzzyCorrection {\n  originalQuery: string;\n  correctedQuery: string;\n  corrections: Array<{\n    original: string;\n    corrected: string;\n    distance: number;\n  }>;\n}\n\nexport interface SearchResponse {\n  query: string;\n  results: SearchResult[];\n  metrics: SearchMetrics;\n  fuzzyCorrection?: FuzzyCorrection;\n}\n\n// ── Community Detection ────────────────────────────────────────\n\nexport interface CommunityEntry {\n  readonly symbolId: string;\n  readonly communityId: number;\n  readonly communityLabel: string;\n}\n\nexport interface GodNode {\n  readonly symbolId: string;\n  readonly bridgedCommunities: readonly number[];\n  readonly centralityScore: number;\n}\n\nexport const EDGE_QUALITY = ['full', 'syntax-only', 'mixed'] as const;\nexport type EdgeQuality = (typeof EDGE_QUALITY)[number];\n\nexport interface CommunitySnapshot {\n  readonly version: 1;\n  readonly computedAt: string;\n  readonly commitSha: string;\n  readonly modularity: number;\n  readonly communities: readonly CommunityEntry[];\n  readonly godNodes: readonly GodNode[];\n  readonly edgeQuality: EdgeQuality;\n  readonly crossClusterEdges: number;\n}\n\nexport interface DriftEvent {\n  readonly symbolId: string;\n  readonly movedFrom: { readonly id: number; readonly label: string };\n  readonly movedTo: { readonly id: number; readonly label: string };\n  readonly firstSeenInNewCluster: string;\n}\n\nexport interface BoundaryViolation {\n  readonly from: {\n    readonly symbolId: string;\n    readonly communityId: number;\n    readonly label: string;\n  };\n  readonly to: {\n    readonly symbolId: string;\n    readonly communityId: number;\n    readonly label: string;\n  };\n  readonly edgeKind: EdgeKind;\n  readonly historicalEdgesBetweenClusters: number;\n  readonly severity: 'high' | 'medium';\n}\n\n// ── Persisted architectural artifacts ──────────────────────────\n// Written by `ctxo index` next to communities.json so the static\n// HTML visualizer can render Architecture views without re-running\n// detectors in the browser.\n\nexport type ConfidenceLevel = 'high' | 'medium' | 'low';\n\nexport interface DriftEventsArtifact {\n  readonly version: 1;\n  readonly computedAt: string;\n  readonly commitSha: string;\n  readonly confidence: ConfidenceLevel;\n  /** The number of history entries passed to the detector (kept for compatibility; confidence is built on `distinctCommits`). */\n  readonly snapshotsAvailable: number;\n  /** Commits other than `commitSha` that the history covers; `confidence` is built on this. */\n  readonly distinctCommits: number;\n  readonly hint?: string;\n  readonly events: readonly DriftEvent[];\n}\n\nexport interface BoundaryViolationsArtifact {\n  readonly version: 1;\n  readonly computedAt: string;\n  readonly commitSha: string;\n  readonly confidence: ConfidenceLevel;\n  /** The number of history entries passed to the detector (kept for compatibility; confidence is built on `distinctCommits`). */\n  readonly snapshotsAvailable: number;\n  /** Commits other than `commitSha` that the history covers; `confidence` is built on this. */\n  readonly distinctCommits: number;\n  readonly hint?: string;\n  readonly violations: readonly 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