@ctxo/cli 0.7.2 → 0.8.1

package/README.md

@@ -10,296 +10,59 @@
   <img alt="Ctxo — Code intelligence for AI agents" src="docs/img/hero-svg.svg" width="100%">
 </picture>
 
-</div>
-
-***
-
-### The Problem
-
-AI coding assistants like Copilot, Claude Code, and Cursor rely on generic tools  `grep`, `find`, file reads to understand your codebase. On brownfield projects with thousands of files, this brute-force exploration creates a chain of problems:
-
-* **Context window saturation** The agent fills its window reading files one by one, leaving little room for actual reasoning
-* **Partial context hallucination** It sees a function but misses its dependencies, leading to wrong assumptions and broken suggestions
-* **Lost-in-the-middle** Critical information buried deep in a long context gets ignored by the model
-* **Context poisoning** Irrelevant code pulled in during exploration biases the model's output
-* **Iteration overhead** Understanding one symbol takes 10-20 tool calls, each adding more noise to the context
-* **Stale reasoning** After too many iterations, the agent contradicts its own earlier assumptions
-
-The result: more tokens burned, slower responses, higher cost, and lower quality output.
-
-### The Solution
-
-Ctxo is an **MCP server** that **enhances** your existing AI tools with dependency-aware, history-enriched code intelligence. Instead of hundreds of `grep` and `read_file` calls, your agent gets the full picture symbol graphs, blast radius, git intent, and risk scores in a **single MCP call**.
-
-* **Clean context** Only relevant symbols and their transitive dependencies, nothing more
-* **Fewer iterations** One call replaces an entire exploration cycle
-* **Higher quality** The agent reasons over structured, complete context instead of fragmented file reads
-
-> A senior developer takes \~10 minutes to gather context across files. Ctxo delivers that same context in **under 500ms**.
-
-## Quick Start
-
-Install the CLI, then run the setup wizard:
-
-```Shell
-npm i -g @ctxo/cli
-ctxo init
-```
-
-That's it. The interactive wizard detects your AI tools, registers the ctxo MCP server in the correct config file (`.mcp.json`, `.vscode/mcp.json`, etc.), generates usage rules so your assistant knows when to call each tool, and prompts to install language plugins it detects in your project (pass `--no-install` to skip).
-
-### Language Plugins
-
-As of v0.7, Ctxo discovers language support from npm packages listed in your project's `package.json`. Three official plugins ship today:
-
 ```Shell
-npm i -D @ctxo/lang-typescript @ctxo/lang-go @ctxo/lang-csharp
+npx @ctxo/init
+npx @ctxo/cli index
 ```
 
-Or install one at a time with the CLI shortcut: `ctxo install typescript` (supports `--yes`, `--global`, `--dry-run`, `--pm`, `--version`). Any package named `@ctxo/lang-*` or `ctxo-lang-*` in your dependencies is auto-loaded.
-
-<details>
-<summary>Manual MCP config (if not using <code>ctxo init</code>)</summary>
-
-**Claude Code / Cursor / Windsurf / Augment / Antigravity** — `.mcp.json`:
-
-```JSON
-{ "mcpServers": { "ctxo": { "command": "npx", "args": ["-y", "@ctxo/cli"] } } }
-```
-
-**VS Code (Copilot)** — `.vscode/mcp.json`:
-
-```JSON
-{ "servers": { "ctxo": { "type": "stdio", "command": "npx", "args": ["-y", "@ctxo/cli"] } } }
-```
-
-**Amazon Q** — `.amazonq/mcp.json`:
-
-```JSON
-{ "mcpServers": { "ctxo": { "command": "npx", "args": ["-y", "@ctxo/cli"] } } }
-```
-
-**Zed** — `settings.json`:
-
-```JSON
-{ "context_servers": { "ctxo": { "command": { "path": "npx", "args": ["-y", "@ctxo/cli"] } } } }
-```
-
-</details>
-
-## 14 Tools
-
-| Tool                        | What it does                                                                             |
-| --------------------------- | ---------------------------------------------------------------------------------------- |
-| `get_logic_slice`           | Symbol + transitive dependencies (L1-L4 progressive detail)                              |
-| `get_blast_radius`          | What breaks if this changes (3-tier: confirmed/likely/potential)                         |
-| `get_architectural_overlay` | Project layer map (Domain/Infrastructure/Adapter)                                        |
-| `get_why_context`           | Git commit intent + anti-pattern warnings (reverts, rollbacks)                           |
-| `get_change_intelligence`   | Complexity x churn composite score                                                       |
-| `find_dead_code`            | Unreachable symbols, unused exports, scaffolding markers                                 |
-| `get_context_for_task`      | Task-optimized context (fix/extend/refactor/understand)                                  |
-| `get_ranked_context`        | Two-phase BM25 search (camelCase-aware, fuzzy correction) + PageRank within token budget |
-| `search_symbols`            | Symbol name/regex search across index (`mode: 'fts'` for BM25)                           |
-| `get_changed_symbols`       | Symbols in recently changed files (git diff)                                             |
-| `find_importers`            | Reverse dependency lookup ("who uses this?")                                             |
-| `get_class_hierarchy`       | Class inheritance tree (ancestors + descendants)                                         |
-| `get_symbol_importance`     | PageRank centrality ranking                                                              |
-| `get_pr_impact`             | Full PR risk assessment in a single call                                                 |
-
-## Tool Selection Guide
-
-```
-Reviewing a PR?           → get_pr_impact
-About to modify code?     → get_blast_radius → get_why_context
-Understanding a symbol?   → get_context_for_task(taskType: "understand")
-Fixing a bug?             → get_context_for_task(taskType: "fix")
-Refactoring?              → get_context_for_task(taskType: "refactor")
-Don't know the name?      → search_symbols or get_ranked_context
-Finding unused code?      → find_dead_code
-Safe to delete?           → find_importers
-Onboarding?               → get_architectural_overlay → get_symbol_importance
-```
+<a href="https://alperhankendi.github.io/Ctxo/docs/">
+  <img src="https://img.shields.io/badge/Get%20Started-%E2%86%92-06b6d4?style=for-the-badge&labelColor=0f172a" alt="Get Started →">
+</a>
 
-## CLI Commands
+<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>
 
-```Shell
-# Setup
-ctxo init                                  # Interactive setup (detects languages, prompts to install plugins, writes AI tool rules, git hooks)
-ctxo init --tools claude-code,cursor -y    # Non-interactive setup
-ctxo init --no-install                     # Skip plugin install prompt
-ctxo init --rules                          # Regenerate AI tool rules only
-ctxo init --dry-run                        # Preview what would be created
-
-# Plugins (v0.7+)
-ctxo install                               # Install plugins for all detected languages
-ctxo install typescript go csharp          # Install specific plugins
-ctxo install typescript --yes --pm pnpm    # CI-friendly, pick package manager
-ctxo install typescript --global --version 0.7.0  # Pin version, install globally
-
-# Indexing
-ctxo index                                 # Build full codebase index
-ctxo index --install-missing               # Auto-install any missing plugins first
-ctxo index --check                         # CI gate: fail if index stale
-ctxo index --skip-history                  # Fast re-index without git history
-ctxo watch                                 # File watcher for incremental re-index
-ctxo sync                                  # Rebuild SQLite cache from committed JSON
-
-# Diagnostics
-ctxo status                                # Show index manifest
-ctxo doctor                                # Health check all subsystems (--json, --quiet)
-ctxo doctor --fix                          # Dependency-ordered auto-remediation (--dry-run, --yes)
-ctxo stats                                 # Show usage statistics (--json, --days N, --clear)
-ctxo --version                             # Print CLI version (--verbose, --json)
-ctxo version                               # Verbose version subcommand (CLI + plugins + runtime)
-```
-
-**Example output:**
-
-```
-ctxo stats
-
-  Usage Summary (all time)
-  ────────────────────────────────────────
-  Total tool calls:      30
-  Total tokens served:   26.0K
-
-  Top Tools
-  ────────────────────────────────────────
-  get_logic_slice         14 calls      avg 352 tokens
-  get_blast_radius        3 calls       avg 1,279 tokens
-  get_ranked_context      3 calls       avg 898 tokens
-  find_importers          2 calls       avg 1,342 tokens
-  get_context_for_task    2 calls       avg 740 tokens
-
-  Top Queried Symbols
-  ────────────────────────────────────────
-  SymbolNode                      15 queries
-  LogicSliceQuery                 4 queries
-  SqliteStorageAdapter            2 queries
-
-  Detail Level Distribution
-  ────────────────────────────────────────
-  L1: ███░░░░░░░   25%
-  L2: ███░░░░░░░   25%
-  L3: ███░░░░░░░   25%
-  L4: ███░░░░░░░   25%
-```
-
-## CI Integration
-
-Keep the committed `.ctxo/index/` in sync with the source tree by failing PRs when the index is stale. Drop-in examples:
-
-- GitHub Actions: [examples/github-actions/ctxo-check.yml](examples/github-actions/ctxo-check.yml)
-- GitLab CI: [examples/gitlab-ci/.gitlab-ci.yml](examples/gitlab-ci/.gitlab-ci.yml)
-
-Both run `ctxo index --check` on every PR/MR. If the index is stale, the job fails and the author runs `ctxo index` locally, then commits the refreshed index. Combined with the `post-commit` hook from `ctxo init`, this keeps the index current without any webhook infrastructure.
-
-## Features
-
-**Response Envelope** All responses include `_meta` with item counts, truncation info, and drill-in hints. Large results auto-truncated at 8KB (configurable via `CTXO_RESPONSE_LIMIT`).
-
-**Intent Filtering** 4 tools accept `intent` parameter for keyword-based result filtering. `get_blast_radius(symbolId, intent: "test")` returns only test-related impacts.
-
-**Tool Annotations** All tools declare `readOnlyHint: true`, `idempotentHint: true`, `openWorldHint: false` for safe auto-approval in agent frameworks.
-
-**Privacy Masking** AWS keys, GCP service accounts, Azure connection strings, JWTs, private IPs, env secrets automatically redacted. Extensible via `.ctxo/masking.json`.
-
-**Interactive Graph** `ctxo visualize` generates a self-contained HTML with vis.js dependency graph. ForceAtlas2 layout, PageRank-based sizing, layer coloring, blast radius on click, git history per symbol, dead code and anti-pattern filters, dark/light theme.
-
-**Debug Mode** `DEBUG=ctxo:*` for all debug output, or `DEBUG=ctxo:git,ctxo:storage` for specific namespaces.
-
-**Per-tool savings vs manual approach:**
-
-```
-                        Manual Tokens   Ctxo Tokens   Savings
-get_logic_slice         ████████ 1,950  █ 150         92%
-get_blast_radius        ███ 800         ██ 600        25%
-get_overlay             ████████████ 25K██ 500        98%
-get_why_context         █ 200           █ 200          0%
-get_change_intelligence ████████ 2,100  ▏ 50          98%
-find_dead_code          █████████ 5,000 ████ 2,000    60%
-────────────────────────────────────────────────────────────
-TOTAL                   35,050 tokens   3,500 tokens  90%
-                        329+ calls      6 calls       98%
-```
-
-## Agentic AI Usage
-
-**Claude Agent SDK:**
-
-```TypeScript
-import { query } from "@anthropic-ai/claude-agent-sdk";
-
-for await (const message of query({
-  prompt: "Analyze the blast radius of AuthService",
-  options: {
-    mcpServers: { ctxo: { command: "npx", args: ["-y", "@ctxo/cli"] } },
-    allowedTools: ["mcp__ctxo__*"]
-  }
-})) { /* ... */ }
-```
-
-**OpenAI Agents SDK:**
+</div>
 
-```Python
-from agents import Agent, Runner
-from agents.mcp import MCPServerStdio
+***
 
-async with MCPServerStdio(params={"command": "npx", "args": ["@ctxo/cli"]}) as ctxo:
-    agent = Agent(name="Reviewer", mcp_servers=[ctxo])
-    result = await Runner.run(agent, "Review the PR impact")
-```
+## The Problem: agents code blind
 
-See [Agentic AI Integration Guide](docs/agentic-ai-integration.md) for LangChain, raw MCP client, and CI/CD examples.
+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.
 
-## Multi-Language Support
+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.
 
-Language support ships as standalone plugins. Install only what your repo needs.
+## The Solution: proactive, not reactive
 
-| Language              | Plugin Package          | Engine                       | Tier   | Toolchain required   | Features                                                                                                           |
-| --------------------- | ----------------------- | ---------------------------- | ------ | -------------------- | ------------------------------------------------------------------------------------------------------------------ |
-| TypeScript/JavaScript | `@ctxo/lang-typescript` | ts-morph                     | Full   | bundled              | Type-aware resolution, cross-file imports, `this.method()` calls, complexity metrics                               |
-| C#                    | `@ctxo/lang-csharp`     | `ctxo-roslyn` (Roslyn)       | Full   | .NET SDK ≥ 8 on PATH | Symbols + `calls` / `uses` / `implements` / `extends`, cross-project resolution, complexity, tree-sitter fallback  |
-| Go                    | `@ctxo/lang-go`         | `ctxo-go-analyzer`           | Full   | Go ≥ 1.22 on PATH    | Symbols + `calls` / `uses` / `implements` / `extends`, reflect-safe dead-code, generics, tree-sitter fallback      |
-| All other languages   | `@ctxo/lang-*` / `ctxo-lang-*` (plugin protocol) | tree-sitter (community adapter) | Syntax | bundled per plugin | Symbol inventory (functions, classes, types, methods), import edges, cyclomatic complexity, unexported symbols    |
+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.**
 
-**Full tier** delivers type-resolved semantic edges across package boundaries — what `get_blast_radius`, `find_importers`, `find_dead_code` and `get_class_hierarchy` actually need. Requires the language's official toolchain on `PATH`; graceful degradation to tree-sitter syntax tier when missing.
+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.
 
-**Syntax tier** works out of the box via the `@ctxo/plugin-api` protocol (v1). Any package named `@ctxo/lang-*` or `ctxo-lang-*` in your dependencies is auto-discovered — third-party plugins can deliver new languages without touching core.
+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?"
 
-## Index Visualizer
+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.
 
-Ctxo ships with an interactive visualizer that renders your codebase index as a dependency graph. Explore symbols, edges, layers, and PageRank scores visually deployed automatically to GitHub Pages on every push.
+## Codebase Dashboard
 
-![1.00](docs/img/ui.png)
+Full-stack analytics UI with eight views: File Tree, Heatmap, Co-Changes, Timeline, Architecture, MCP Explorer, and Diff. Deployed to GitHub Pages on every push.
 
-[Open Live Visualizer](https://alperhankendi.github.io/Ctxo/ctxo-visualizer.html)
+![Codebase Dashboard](docs/img/ui.png)
 
-## How It Works
+[Open Dashboard](https://alperhankendi.github.io/Ctxo/ctxo-visualizer.html)
 
-<img src="docs/img/mcp-server.png" alt="Ctxo MCP Server Architecture" width="400">
+## Dependency Graph
 
-Ctxo builds a **committed JSON index** (`.ctxo/index/`) that captures symbols, dependency edges, git history, and co-change data. The MCP server reads this index to answer queries no runtime parsing, no external services.
+`ctxo visualize` generates a self-contained HTML from your `.ctxo/` index. Interactive force-directed graph with PageRank sizing, layer coloring, blast radius on click, and dark/light theme.
 
-The codebase is a pnpm monorepo with 5 packages: `@ctxo/cli` (this package), `@ctxo/plugin-api` (plugin protocol v1), and three official language plugins (`@ctxo/lang-typescript`, `@ctxo/lang-go`, `@ctxo/lang-csharp`).
+![Dependency Graph](docs/img/visualize-00-light.png)
 
-```
-.ctxo/
-  index/          ← committed (per-file JSON, reviewable in PRs)
-  .cache/         ← gitignored (local SQLite, auto-rebuilt)
-  config.yaml     ← committed (team settings)
-  masking.json    ← committed (custom masking patterns)
-```
+[Open Dependency Graph](https://alperhankendi.github.io/Ctxo/visualize.html)
 
 ## Links
 
+* [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)
-* [MCP Validation Runbook](docs/runbook/mcp-validation/mcp-validation.md)
-* [CLI Validation Runbook](docs/runbook/cli-validation/cli-validation.md)
-* [Architecture](docs/artifacts/architecture.md)
-* [PRD](docs/artifacts/prd.md)
 
 ## License
 

package/dist/atomic-write-AQNYJFAG.js

@@ -0,0 +1,10 @@
+#!/usr/bin/env node
+import {
+  atomicWrite,
+  sweepStaleTmpFiles
+} from "./chunk-6EKERTJ7.js";
+export {
+  atomicWrite,
+  sweepStaleTmpFiles
+};
+//# sourceMappingURL=atomic-write-AQNYJFAG.js.map

package/dist/{chunk-WXA2JJLH.js → chunk-2TVHKCCU.js}

@@ -132,8 +132,9 @@ var JsonIndexReader = class {
       if (entry.isSymbolicLink()) continue;
       const fullPath = join(dir, entry.name);
       if (entry.isDirectory()) {
+        if (entry.name === "communities.history") continue;
         files.push(...this.collectJsonFiles(fullPath, visited));
-      } else if (entry.name.endsWith(".json") && entry.name !== "co-changes.json") {
+      } 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") {
         files.push(fullPath);
       }
     }
@@ -145,4 +146,4 @@ export {
   DetailLevelSchema,
   JsonIndexReader
 };
-//# sourceMappingURL=chunk-WXA2JJLH.js.map
+//# sourceMappingURL=chunk-2TVHKCCU.js.map

package/dist/chunk-2TVHKCCU.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 { FileIndexSchema, type FileIndex } from '../../core/types.js';\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    if (!existsSync(this.indexDir)) {\n      return [];\n    }\n\n    const jsonFiles = this.collectJsonFiles(this.indexDir);\n    const results: FileIndex[] = [];\n\n    for (const filePath of jsonFiles) {\n      const parsed = this.readSingle(filePath);\n      if (parsed) {\n        results.push(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        const rel = relative(this.indexDir, absolutePath);\n        console.error(\n          `[ctxo:json-reader] Invalid schema in ${rel}: ${result.error.message}`,\n        );\n        return undefined;\n      }\n\n      return result.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 === 'communities.history') continue;\n        files.push(...this.collectJsonFiles(fullPath, visited));\n      } else if (\n        entry.name.endsWith('.json') &&\n        entry.name !== 'co-changes.json' &&\n        entry.name !== 'communities.json' &&\n        entry.name !== 'drift-events.json' &&\n        entry.name !== 'boundary-violations.json'\n      ) {\n        files.push(fullPath);\n      }\n    }\n\n    return files;\n  }\n}\n","import { z } from 'zod';\n\n// ── Symbol Kinds ────────────────────────────────────────────────\n\nexport const SYMBOL_KINDS = [\n  'function',\n  'class',\n  'interface',\n  'method',\n  'variable',\n  'type',\n] as const;\n\nexport const SymbolKindSchema = z.enum(SYMBOL_KINDS);\nexport type SymbolKind = z.infer<typeof SymbolKindSchema>;\n\n// ── Edge Kinds ──────────────────────────────────────────────────\n\nexport const EDGE_KINDS = [\n  'imports',\n  'calls',\n  'extends',\n  'implements',\n  'uses',\n] as const;\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// ── 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  })\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,\n  to: SymbolIdSchema,\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// ── 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});\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?: 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package/dist/chunk-6EKERTJ7.js

@@ -0,0 +1,80 @@
+#!/usr/bin/env node
+
+// src/adapters/storage/atomic-write.ts
+import { readdirSync, renameSync, statSync, unlinkSync, writeFileSync, existsSync } from "fs";
+import { join } from "path";
+
+// src/core/logger.ts
+function isDebugEnabled(namespace) {
+  const debugEnv = process.env["DEBUG"] ?? "";
+  if (!debugEnv) return false;
+  const patterns = debugEnv.split(",").map((p) => p.trim());
+  return patterns.some((p) => {
+    if (p === "*" || p === "ctxo:*") return true;
+    if (p === namespace) return true;
+    if (p.endsWith(":*") && namespace.startsWith(p.slice(0, -1))) return true;
+    return false;
+  });
+}
+function createLogger(namespace) {
+  const prefix = `[${namespace}]`;
+  return {
+    debug(message, ...args) {
+      if (isDebugEnabled(namespace)) {
+        console.error(`${prefix} DEBUG ${message}`, ...args);
+      }
+    },
+    info(message, ...args) {
+      console.error(`${prefix} ${message}`, ...args);
+    },
+    warn(message, ...args) {
+      console.error(`${prefix} WARN ${message}`, ...args);
+    },
+    error(message, ...args) {
+      console.error(`${prefix} ERROR ${message}`, ...args);
+    }
+  };
+}
+
+// src/adapters/storage/atomic-write.ts
+var log = createLogger("ctxo:storage");
+var TMP_SUFFIX_RE = /\.\d+\.tmp$/;
+var TMP_STALE_THRESHOLD_MS = 6e4;
+function atomicWrite(targetPath, content) {
+  const tmpPath = `${targetPath}.${process.pid}.tmp`;
+  writeFileSync(tmpPath, content, "utf-8");
+  renameSync(tmpPath, targetPath);
+}
+function sweepStaleTmpFiles(dir, now = Date.now()) {
+  if (!existsSync(dir)) return 0;
+  let cleaned = 0;
+  try {
+    for (const entry of readdirSync(dir, { withFileTypes: true })) {
+      if (entry.isSymbolicLink()) continue;
+      if (entry.isDirectory()) {
+        cleaned += sweepStaleTmpFiles(join(dir, entry.name), now);
+        continue;
+      }
+      if (!TMP_SUFFIX_RE.test(entry.name)) continue;
+      const full = join(dir, entry.name);
+      try {
+        const age = now - statSync(full).mtimeMs;
+        if (age < TMP_STALE_THRESHOLD_MS) continue;
+        unlinkSync(full);
+        cleaned++;
+      } catch (err) {
+        log.error(`failed to sweep ${entry.name}: ${err.message}`);
+      }
+    }
+  } catch (err) {
+    log.error(`failed to scan ${dir}: ${err.message}`);
+  }
+  return cleaned;
+}
+
+export {
+  createLogger,
+  atomicWrite,
+  sweepStaleTmpFiles
+};
+//# sourceMappingURL=chunk-6EKERTJ7.js.map

package/dist/chunk-6EKERTJ7.js.map

@@ -0,0 +1 @@
+{"version":3,"sources":["../src/adapters/storage/atomic-write.ts","../src/core/logger.ts"],"sourcesContent":["import { readdirSync, renameSync, statSync, unlinkSync, writeFileSync, existsSync } from 'node:fs';\nimport { join } from 'node:path';\n\nimport { createLogger } from '../../core/logger.js';\n\nconst log = createLogger('ctxo:storage');\n\nconst TMP_SUFFIX_RE = /\\.\\d+\\.tmp$/;\nconst TMP_STALE_THRESHOLD_MS = 60_000; // anything older than 60 s is from a dead process\n\nexport function atomicWrite(targetPath: string, content: string): void {\n  const tmpPath = `${targetPath}.${process.pid}.tmp`;\n  writeFileSync(tmpPath, content, 'utf-8');\n  renameSync(tmpPath, targetPath);\n}\n\n/**\n * Remove orphaned .<pid>.tmp files left behind when a previous write crashed\n * (SIGKILL / power loss / ENOSPC). Only files older than a threshold are\n * removed so we never race a concurrent writer.\n *\n * Safe to call on every startup — walks the supplied directory non-recursively.\n */\nexport function sweepStaleTmpFiles(dir: string, now: number = Date.now()): number {\n  if (!existsSync(dir)) return 0;\n  let cleaned = 0;\n  try {\n    for (const entry of readdirSync(dir, { withFileTypes: true })) {\n      if (entry.isSymbolicLink()) continue;\n      if (entry.isDirectory()) {\n        cleaned += sweepStaleTmpFiles(join(dir, entry.name), now);\n        continue;\n      }\n      if (!TMP_SUFFIX_RE.test(entry.name)) continue;\n      const full = join(dir, entry.name);\n      try {\n        const age = now - statSync(full).mtimeMs;\n        if (age < TMP_STALE_THRESHOLD_MS) continue;\n        unlinkSync(full);\n        cleaned++;\n      } catch (err) {\n        log.error(`failed to sweep ${entry.name}: ${(err as Error).message}`);\n      }\n    }\n  } catch (err) {\n    log.error(`failed to scan ${dir}: ${(err as Error).message}`);\n  }\n  return cleaned;\n}\n","/**\n * Structured logger for Ctxo — all output goes to stderr (stdout reserved for MCP JSON-RPC).\n *\n * Supports debug mode via DEBUG environment variable:\n *   DEBUG=ctxo:*          — all debug output\n *   DEBUG=ctxo:git        — only git adapter debug\n *   DEBUG=ctxo:index      — only indexing debug\n *   DEBUG=ctxo:mcp        — only MCP handler debug\n *   DEBUG=ctxo:storage    — only storage adapter debug\n *   DEBUG=ctxo:masking    — only masking pipeline debug\n *\n * Always outputs: info, warn, error (regardless of DEBUG).\n * Only outputs debug when matching namespace is enabled.\n */\n\nfunction isDebugEnabled(namespace: string): boolean {\n  const debugEnv = process.env['DEBUG'] ?? 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