Merge branch 'main' into fix/add-gnu-source-for-strcasestr

Author: DeusData

CONTRIBUTING.md

@@ -85,14 +85,45 @@ Language support is split between two layers:
 4. Add a test case in `tests/test_pipeline.c` for integration-level fixes
 5. Verify with a real open-source repo
 
+### Infrastructure Languages (Infra-Pass Pattern)
+
+Languages like **Dockerfile**, **docker-compose**, **Kubernetes manifests**, and **Kustomize** do not require a new tree-sitter grammar. Instead they follow an *infra-pass* pattern, reusing the existing tree-sitter YAML grammar where applicable:
+
+1. **Detection helpers** in `src/pipeline/pass_infrascan.c` — functions like `cbm_is_dockerfile()`, `cbm_is_k8s_manifest()`, `cbm_is_kustomize_file()` identify files by name and/or content heuristics (e.g., presence of `apiVersion:`).
+2. **Custom extractors** in `internal/cbm/extract_k8s.c` — tree-sitter-based parsers that walk the YAML AST (using the tree-sitter YAML grammar) and populate `CBMFileResult` with imports and definitions.
+3. **Pipeline pass** (`pass_k8s.c`, `pass_infrascan.c`) — calls the extractor and emits graph nodes/edges. K8s manifests emit `Resource` nodes; Kustomize files emit `Module` nodes with `IMPORTS` edges to referenced resource files.
+
+**When adding a new infrastructure language:**
+- Add a detection helper (`cbm_is_<lang>_file()`) in `pass_infrascan.c` or a new `pass_<lang>.c`.
+- Add the `CBM_LANG_<LANG>` enum value in `internal/cbm/cbm.h` and a row in the language table in `lang_specs.c`.
+- Write a custom extractor that returns `CBMFileResult*` — do not add a tree-sitter grammar.
+- Register the pass in `pipeline.c`.
+- Add tests in `tests/test_pipeline.c` following the `TEST(infra_is_dockerfile)` and `TEST(k8s_extract_manifest)` patterns.
+
+## Commit Format
+
+Use conventional commits: `type(scope): description`
+
+| Type | When to use |
+|------|-------------|
+| `feat` | New feature or capability |
+| `fix` | Bug fix |
+| `test` | Adding or updating tests |
+| `refactor` | Code change that neither fixes a bug nor adds a feature |
+| `perf` | Performance improvement |
+| `docs` | Documentation only |
+| `chore` | Build scripts, CI, dependency updates |
+
+Examples: `fix(store): set busy_timeout before WAL`, `feat(cli): add --progress flag`
+
 ## Pull Request Guidelines
 
+- **One issue per PR.** Each PR must address exactly one bug, one feature, or one refactor. Do not bundle multiple fixes or feature additions into a single PR. If your change touches multiple areas, split it into separate PRs.
+- **Open an issue first.** Every PR should reference a tracking issue (`Fixes #N` or `Closes #N`). This ensures the change is discussed before code is written.
 - **C code only** — this project was rewritten from Go to pure C in v0.5.0. Go PRs will be acknowledged and potentially ported, but cannot be merged directly.
-- One logical change per PR — don't bundle unrelated features
 - Include tests for new functionality
 - Run `scripts/test.sh` and `scripts/lint.sh` before submitting
 - Keep PRs focused — avoid unrelated reformatting or refactoring
-- Reference the issue number in your PR description
 
 ## Security
 

Makefile.cbm

@@ -115,6 +115,7 @@ EXTRACTION_SRCS = \
     $(CBM_DIR)/extract_type_refs.c \
     $(CBM_DIR)/extract_type_assigns.c \
     $(CBM_DIR)/extract_env_accesses.c \
+    $(CBM_DIR)/extract_k8s.c \
     $(CBM_DIR)/helpers.c \
     $(CBM_DIR)/lang_specs.c
 
@@ -148,6 +149,7 @@ MCP_SRCS = src/mcp/mcp.c
 # Discover module (new)
 DISCOVER_SRCS = \
     src/discover/language.c \
+    src/discover/userconfig.c \
     src/discover/gitignore.c \
     src/discover/discover.c
 
@@ -176,6 +178,7 @@ PIPELINE_SRCS = \
     src/pipeline/pass_envscan.c \
     src/pipeline/pass_compile_commands.c \
     src/pipeline/pass_infrascan.c \
+    src/pipeline/pass_k8s.c \
     src/pipeline/httplink.c
 
 # Traces module (new)
@@ -259,6 +262,7 @@ TEST_MCP_SRCS = \
 
 TEST_DISCOVER_SRCS = \
     tests/test_language.c \
+    tests/test_userconfig.c \
     tests/test_gitignore.c \
     tests/test_discover.c
 

README.md

@@ -4,15 +4,15 @@
 [![License](https://img.shields.io/badge/license-MIT-green)](LICENSE)
 [![CI](https://img.shields.io/github/actions/workflow/status/DeusData/codebase-memory-mcp/dry-run.yml?label=CI)](https://github.com/DeusData/codebase-memory-mcp/actions/workflows/dry-run.yml)
 [![Tests](https://img.shields.io/badge/tests-2042_passing-brightgreen)](https://github.com/DeusData/codebase-memory-mcp)
-[![Languages](https://img.shields.io/badge/languages-64-orange)](https://github.com/DeusData/codebase-memory-mcp)
+[![Languages](https://img.shields.io/badge/languages-66-orange)](https://github.com/DeusData/codebase-memory-mcp)
 [![Agents](https://img.shields.io/badge/agents-10-purple)](https://github.com/DeusData/codebase-memory-mcp)
 [![Pure C](https://img.shields.io/badge/pure_C-zero_dependencies-blue)](https://github.com/DeusData/codebase-memory-mcp)
 [![Platform](https://img.shields.io/badge/macOS_%7C_Linux_%7C_Windows-supported-lightgrey)](https://github.com/DeusData/codebase-memory-mcp/releases/latest)
 [![OpenSSF Scorecard](https://api.scorecard.dev/projects/github.com/DeusData/codebase-memory-mcp/badge)](https://scorecard.dev/viewer/?uri=github.com/DeusData/codebase-memory-mcp)
 
 **The fastest and most efficient code intelligence engine for AI coding agents.** Full-indexes an average repository in milliseconds, the Linux kernel (28M LOC, 75K files) in 3 minutes. Answers structural queries in under 1ms. Ships as a single static binary for macOS, Linux, and Windows — download, run `install`, done.
 
-High-quality parsing through [tree-sitter](https://tree-sitter.github.io/tree-sitter/) AST analysis across all 64 languages, enhanced with LSP-style hybrid type resolution for Go, C, and C++ (more languages coming soon) — producing a persistent knowledge graph of functions, classes, call chains, HTTP routes, and cross-service links. 14 MCP tools. Zero dependencies. Plug and play across 10 coding agents.
+High-quality parsing through [tree-sitter](https://tree-sitter.github.io/tree-sitter/) AST analysis across all 66 languages, enhanced with LSP-style hybrid type resolution for Go, C, and C++ (more languages coming soon) — producing a persistent knowledge graph of functions, classes, call chains, HTTP routes, and cross-service links. 14 MCP tools. Zero dependencies. Plug and play across 10 coding agents.
 
 <p align="center">
   <img src="docs/graph-ui-screenshot.png" alt="Graph visualization UI showing the codebase-memory-mcp knowledge graph" width="800">
@@ -24,10 +24,11 @@ High-quality parsing through [tree-sitter](https://tree-sitter.github.io/tree-si
 
 - **Extreme indexing speed** — Linux kernel (28M LOC, 75K files) in 3 minutes. RAM-first pipeline: LZ4 compression, in-memory SQLite, fused Aho-Corasick pattern matching. Memory released after indexing.
 - **Plug and play** — single static binary for macOS (arm64/amd64), Linux (arm64/amd64), and Windows (amd64). No Docker, no runtime dependencies, no API keys. Download → `install` → restart agent → done.
-- **64 languages** — vendored tree-sitter grammars compiled into the binary. Nothing to install, nothing that breaks.
+- **66 languages** — vendored tree-sitter grammars compiled into the binary. Nothing to install, nothing that breaks.
 - **120x fewer tokens** — 5 structural queries: ~3,400 tokens vs ~412,000 via file-by-file search. One graph query replaces dozens of grep/read cycles.
 - **10 agents, one command** — `install` auto-detects Claude Code, Codex CLI, Gemini CLI, Zed, OpenCode, Antigravity, Aider, KiloCode, VS Code, and OpenClaw — configures MCP entries, instruction files, and pre-tool hooks for each.
 - **Built-in graph visualization** — 3D interactive UI at `localhost:9749` (optional UI binary variant).
+- **Infrastructure-as-code indexing** — Dockerfiles, Kubernetes manifests, and Kustomize overlays indexed as graph nodes with cross-references. `Resource` nodes for K8s kinds, `Module` nodes for Kustomize overlays with `IMPORTS` edges to referenced resources.
 - **14 MCP tools** — search, trace, architecture, impact analysis, Cypher queries, dead code detection, cross-service HTTP linking, ADR management, and more.
 
 ## Quick Start
@@ -279,7 +280,7 @@ codebase-memory-mcp cli --raw search_graph '{"label": "Function"}' | jq '.result
 
 ### Node Labels
 
-`Project`, `Package`, `Folder`, `File`, `Module`, `Class`, `Function`, `Method`, `Interface`, `Enum`, `Type`, `Route`
+`Project`, `Package`, `Folder`, `File`, `Module`, `Class`, `Function`, `Method`, `Interface`, `Enum`, `Type`, `Route`, `Resource`
 
 ### Edge Types
 
@@ -306,6 +307,24 @@ codebase-memory-mcp config set auto_index_limit 50000    # max files for auto-in
 codebase-memory-mcp config reset auto_index              # reset to default
 ```
 
+## Custom File Extensions
+
+Map additional file extensions to supported languages via JSON config files. Useful for framework-specific extensions like `.blade.php` (Laravel) or `.mjs` (ES modules).
+
+**Per-project** (in your repo root):
+```json
+// .codebase-memory.json
+{"extra_extensions": {".blade.php": "php", ".mjs": "javascript"}}
+```
+
+**Global** (applies to all projects):
+```json
+// ~/.config/codebase-memory-mcp/config.json  (or $XDG_CONFIG_HOME/...)
+{"extra_extensions": {".twig": "html", ".phtml": "php"}}
+```
+
+Project config overrides global for conflicting extensions. Unknown language values are silently skipped. Missing config files are ignored.
+
 ## Persistence
 
 SQLite databases stored at `~/.cache/codebase-memory-mcp/`. Persists across restarts (WAL mode, ACID-safe). To reset: `rm -rf ~/.cache/codebase-memory-mcp/`.
@@ -323,7 +342,7 @@ SQLite databases stored at `~/.cache/codebase-memory-mcp/`. Persists across rest
 
 ## Language Support
 
-64 languages. Benchmarked against 64 real open-source repositories (78 to 49K nodes):
+66 languages. Benchmarked against 64 real open-source repositories (78 to 49K nodes):
 
 | Tier | Score | Languages |
 |------|-------|-----------|
@@ -348,7 +367,7 @@ src/
   traces/             Runtime trace ingestion
   ui/                 Embedded HTTP server + 3D graph visualization
   foundation/         Platform abstractions (threads, filesystem, logging, memory)
-internal/cbm/         Vendored tree-sitter grammars (64 languages) + AST extraction engine
+internal/cbm/         Vendored tree-sitter grammars (66 languages) + AST extraction engine
 ```
 
 ## License

internal/cbm/cbm.c

@@ -316,6 +316,11 @@ CBMFileResult *cbm_extract_file(const char *source, int source_len, CBMLanguage
     cbm_extract_imports(&ctx);
     cbm_extract_unified(&ctx);
 
+    // K8s / Kustomize semantic pass (additional structured extraction for YAML-based infra files).
+    if (ctx.language == CBM_LANG_KUSTOMIZE || ctx.language == CBM_LANG_K8S) {
+        cbm_extract_k8s(&ctx);
+    }
+
     // LSP type-aware call resolution
     uint64_t lsp_start = now_ns();
     if (language == CBM_LANG_GO) {

internal/cbm/cbm.h

@@ -75,6 +75,8 @@ typedef enum {
     CBM_LANG_FORM,
     CBM_LANG_MAGMA,
     CBM_LANG_WOLFRAM,
+    CBM_LANG_KUSTOMIZE, // kustomization.yaml — Kubernetes overlay tool
+    CBM_LANG_K8S,       // Generic Kubernetes manifest (apiVersion: detected)
     CBM_LANG_COUNT
 } CBMLanguage;
 
@@ -361,4 +363,7 @@ void cbm_extract_type_assigns(CBMExtractCtx *ctx);
 // Single-pass unified extraction (replaces the 7 calls above except defs+imports).
 void cbm_extract_unified(CBMExtractCtx *ctx);
 
+// K8s / Kustomize semantic extractor (called when language is CBM_LANG_K8S or CBM_LANG_KUSTOMIZE).
+void cbm_extract_k8s(CBMExtractCtx *ctx);
+
 #endif // CBM_H