Platform

Claude Code

context-mode version

1.0.148

Debug script output (REQUIRED)

{
  "context_mode": {
    "version": "1.0.148",
    "binary_path": "C:\\Users\\<user>\\AppData\\Roaming\\npm\\node_modules\\context-mode\\",
    "available_commands": ["doctor", "upgrade", "hook", "statusline"]
  },
  "runtime": {
    "node": "v25.9.0",
    "bun": "1.3.14",
    "npm": "11.12.1",
    "perl": "v5.38.2",
    "python": "3.14.4",
    "shell": "GNU bash 5.2.37 (Git Bash msys)"
  },
  "os": {
    "platform": "Windows 11 Pro",
    "version": "10.0.26200",
    "arch": "x64"
  },
  "doctor_output": {
    "platform_detection": "Claude Code (high confidence)",
    "storage_sessions": "C:\\Users\\<user>\\.claude\\context-mode\\sessions",
    "storage_content": "C:\\Users\\<user>\\.claude\\context-mode\\content",
    "storage_stats": "C:\\Users\\<user>\\.claude\\context-mode\\sessions",
    "performance": "FAST (Bun detected)",
    "language_coverage": "5/11 (45%) — javascript, shell, typescript, python, perl",
    "server_test": "PASS",
    "hooks_configured": ["PreToolUse", "SessionStart"],
    "hook_scripts_pass": ["pretooluse", "posttooluse", "precompact", "sessionstart", "userpromptsubmit"],
    "plugin_cache_integrity": "PASS",
    "plugin_enabled": "PASS — context-mode@context-mode",
    "hook_config_portability": "PASS — .github/hooks/context-mode.json (no hard-coded paths)",
    "fts5_sqlite": "PASS"
  }
}

Exact prompt that triggered the bug (REQUIRED)

Run ctx_index on the project root directory:

ctx_index(path: "<project-root>")

Then verify the same behavior on any other absolute directory path
(e.g. "C:\\Users\\me\\repo" or "/home/user/project").

Full error output (REQUIRED)

Tool: ctx_index
Input: { "path": "<project-root>" }
Output: Index error: refusing to index d:\Desenvolvimento\Agent_Kit: not a regular file

Reproduced verbatim on FOUR independent client/model combinations
running v1.0.148 with Bun 1.3.14 on the same Windows 11 host:

┌────────────────────────────────────┬──────────────────────────────────────────────────────────────────┐
│ Client                             │ Result                                                           │
├────────────────────────────────────┼──────────────────────────────────────────────────────────────────┤
│ Claude Code (Opus 4.7)             │ "Index error: refusing to index <project-root>:    │
│ npm global install                 │  not a regular file" — 0 files processed                         │
├────────────────────────────────────┼──────────────────────────────────────────────────────────────────┤
│ Codex CLI (GPT-5)                  │ Same error — 0 files processed, took 0.114s                      │
│ npm global install                 │                                                                  │
├────────────────────────────────────┼──────────────────────────────────────────────────────────────────┤
│ Antigravity (Gemini 3.5 Flash)     │ Same error — 0 files                                             │
│ Bundled at                         │                                                                  │
│ .gemini/antigravity-ide/mcp/       │                                                                  │
├────────────────────────────────────┼──────────────────────────────────────────────────────────────────┤
│ Antigravity (Gemini 3.1 Pro)       │ Same error — 0 files (~0.000s, fail instant)                     │
│ Same bundled install               │                                                                  │
└────────────────────────────────────┴──────────────────────────────────────────────────────────────────┘

No stack trace surfaces to the MCP client; the rejection happens before
any traversal logic runs. The error string ("not a regular file")
strongly suggests an `fs.statSync().isFile()` check that returns early
without attempting recursive walk.

We also re-ran the same prompts on v1.0.146 before upgrading to v1.0.148
(same 4 clients) — identical error in all 8 runs. The 1.0.146 → 1.0.148
upgrade did NOT touch this behavior.

Steps to reproduce (REQUIRED)

1. Install / upgrade:
   npm install -g context-mode@1.0.148

2. (Optional) Install Bun for FAST performance — reproduces with or without:
   powershell -c "irm bun.sh/install.ps1 | iex"

3. Configure MCP in any client. Examples:

   • Claude Code: claude mcp add --transport stdio --scope user context-mode -- bun x context-mode
   • Codex CLI: [mcp_servers.context-mode]\n command = "bun"\n args = ["x","context-mode"]
   • Antigravity: ~/.gemini/config/mcp_config.json → { "mcpServers": { "context-mode": { "command": "bun", "args": ["x","context-mode"] } } }

4. From any agent session, call:
   ctx_index(path: "")

5. Observe error:
   Index error: refusing to index : not a regular file

6. Confirm that a file path works (proves the bug is the dir branch, not perms):
   ctx_index(path: "/README.md") → succeeds, returns sections count

What have you tried to fix it?

1. Verified across 4 client/model combinations on Windows 11 with both
   v1.0.146 and v1.0.148 — behavior is server-side and identical, ruling
   out client adapter issues.

2. Inspected installed CLI surface: context-mode --help exposes only
   doctor, upgrade, hook, statusline. No index subcommand to
   bypass the MCP path. No scripts/ctx-debug.sh shipped (the script
   this issue template requests does not exist in npm install).

3. Verified bun-mode does not change the behavior — error is byte-identical
   with and without Bun, with and without our wrapper installer.

4. Workarounds attempted, all brittle:
   a) Have the agent shell out (Glob / find / Get-ChildItem) and loop
   ctx_index per file. This works but caps real-world value:
   across our 4 test clients, agents indexed only 0–11 individual
   files manually before giving up.
   b) Use ctx_search with array of queries — does NOT replace indexing,
   only batches search over already-indexed content.
   c) Use ctx_batch_execute — surprise gotcha: its queries parameter
   is scoped only to the batch's own output, NOT the global index
   (the tool's own tip confirms: "Results are scoped to this batch
   only. To search across all indexed sources, use ctx_search").

5. Measured impact: cache hit rate / token savings correlate directly
   with how many files the agent successfully indexed manually:

   ┌──────────────────────┬─────────────┬──────────────┬──────────────────────┐
   │ Client (v1.0.148) │ Files mgr. │ Tokens saved │ Reduction │
   │ │ indexed │ in session │ │
   ├──────────────────────┼─────────────┼──────────────┼──────────────────────┤
   │ Antigravity (Flash) │ 11 │ 27.1K │ 88.1% │
   │ Claude Code (Opus) │ 5 │ 15.1K │ 79.8% │
   │ Codex CLI (GPT-5) │ 0 │ 8.2K │ 46.0% │
   │ Antigravity (Pro) │ 0 │ NEG (86→80%) │ regression! │
   └──────────────────────┴─────────────┴──────────────┴──────────────────────┘

   In the worst case (Antigravity Pro), querying without a real index
   actually DECREASED the cache ratio because queries consumed more
   tokens than they saved. Project-wide indexing is the missing
   feature that closes this gap.

Expected behavior:

ctx_index(path: "") should walk the directory respecting:
- a default ignore list (node_modules, .git, dist, build, .next, etc.)
- optional include / exclude glob arrays
- optional maxDepth and maxFiles to prevent runaway
- optional extensions filter (default to .md, .mjs, .js, .ts,
.py, .json, etc.)

This matches every comparable indexer (ripgrep, fd, tree-sitter
walkers, LlamaIndex SimpleDirectoryReader, etc.) and is the obvious
user expectation given the tool's name.

Proposed PR shape (happy to implement if approach is approved):

1. In ctx_index handler, detect fs.statSync(path).isDirectory().
2. If directory, call new indexDirectory(path, opts) that:
   • uses fs.readdir({ recursive: true }) (Node 20+) or fast-glob
   • applies default ignore + user-provided include/exclude
   • calls existing per-file index path in parallel
     (concurrency cap, e.g. 8)
   • aggregates and returns { filesIndexed, sectionsIndexed,
     durationMs, skipped, errors }.
3. Backwards-compatible: file paths still go through the original
   code path unchanged.
4. Tests: regular file (existing green), directory defaults,
   directory with ignore, empty directory, non-existent path, deeply
   nested directory with maxDepth.

Happy to open a PR against next branch — confirm the API shape
(opts.include / opts.exclude / opts.maxDepth / opts.maxFiles
/ opts.extensions) and I'll write it.

Pre-submission checklist

• I have run the debug script and pasted the output above
• I am using the latest version of context-mode
• I have searched existing issues for duplicates
• I have included steps to reproduce the issue

Operating System

Windows (PowerShell)

JS Runtime

Bun 1.3.14 (also reproduced with Node 25.9.0 fallback before installing Bun)