Sync main with release/0.2.579 (api.wiki.codes MCP, 1h MCP timeout, C parser, extension parsers, bench/snapshot perf)

README.md

@@ -36,7 +36,8 @@
 > **Alpha software — API is stabilizing but may change**
 >
 > codedb works and is used daily in production AI workflows, but:
-> - **Language support** — Zig, Python, TypeScript/JavaScript, Rust, Go, PHP, Ruby, HCL, R, Dart/Flutter
+> - **Parser support** — Zig, C/C++, Python, TypeScript/JavaScript, Rust, Go, PHP, Ruby, HCL, R, Dart/Flutter
+> - **Lightweight outline support** — Java, Kotlin, Svelte, Vue, Astro, shell, CSS/SCSS, SQL, protobuf, Fortran, LLVM IR, MLIR, and TableGen
 > - **No auth** — HTTP server binds to localhost only
 > - **Snapshot format** may change between versions
 > - **MCP protocol** is JSON-RPC 2.0 over stdio (stable)
@@ -53,7 +54,7 @@
 | Auto-registration in Claude, Codex, Gemini, Cursor     |                                          |
 | Polling file watcher with filtered directory walker    |                                          |
 | Portable snapshot for instant MCP startup              |                                          |
-| Singleton MCP with PID lock + 10min idle timeout       |                                          |
+| Singleton MCP with PID lock + 1h idle timeout          |                                          |
 | Sensitive file blocking (.env, credentials, keys)      |                                          |
 | Codesigned + notarized macOS binaries                  |                                          |
 | SHA256 checksum verification in installer              |                                          |
@@ -137,25 +138,30 @@ codedb hot                            # recently modified files
 
 ### `codedb_remote` — Cloud Intelligence
 
-Query any public GitHub repo without cloning it. Powered by `codedb.codegraff.com`.
+Query any public GitHub repo without cloning it. The default backend uses `codedb.codegraff.com`; `backend="wiki"` uses `api.wiki.codes` for code intelligence plus dependency/security artifacts.
 
 ```
-# Get the file tree of an external repo
+# Get the file tree of an external repo via the default backend
 codedb_remote repo="vercel/next.js" action="tree"
 
 # Search for code in a dependency
 codedb_remote repo="justrach/merjs" action="search" query="handleRequest"
 
-# Get symbol outlines
-codedb_remote repo="justrach/merjs" action="outline"
+# Exact symbol lookup through api.wiki.codes
+codedb_remote repo="justrach/codedb" backend="wiki" action="symbol" query="buildSnapshot"
 
-# Get repo metadata
-codedb_remote repo="justrach/merjs" action="meta"
+# Check dependency CVE evidence; scope can be runtime or all
+codedb_remote repo="axios/axios" backend="wiki" action="cves" scope="runtime"
+
+# Raw wiki slugs are accepted for repos that are indexed that way
+codedb_remote repo="chromium" backend="wiki" action="policy"
 ```
 
-**Actions:** `tree`, `outline`, `search`, `meta`
+**Default actions:** `tree`, `outline`, `search`, `meta`
+
+**Wiki actions:** `tree`, `outline`, `search`, `symbol`, `policy`, `deps`, `score`, `cves`, `commits`, `branches`, `dep-history`
 
-**Note:** This tool calls `codedb.codegraff.com` via HTTPS. No API key required. The service must be available for this tool to work.
+**Note:** This tool calls remote HTTPS services. No API key required. The selected service must be available for this tool to work.
 
 ### CLI Commands
 

docs/architecture.md

@@ -136,7 +136,7 @@ JSON-RPC 2.0 over stdio with Content-Length framing. Implements the Model Contex
 | `codedb_status` | Index status |
 | `codedb_snapshot` | Full snapshot |
 | `codedb_bundle` | Batch multiple queries (max 20 ops) |
-| `codedb_remote` | Query GitHub repos via codedb.codegraff.com |
+| `codedb_remote` | Query GitHub repos via codedb.codegraff.com or api.wiki.codes |
 | `codedb_projects` | List locally indexed projects |
 | `codedb_index` | Index a local folder |
 **Safety:** path validation, oversized message handling (drains >1MB lines instead of killing the loop).

scripts/compare-bench.py

@@ -28,18 +28,28 @@ def pct_change(base_ns: int, head_ns: int) -> float:
     return ((head_ns - base_ns) / base_ns) * 100.0
 
 
-def render_markdown(rows: list[tuple[str, int, int, float]], threshold_pct: float) -> str:
+def status_for(delta_pct: float, abs_delta_ns: int, threshold_pct: float, min_abs_ns: int) -> str:
+    if delta_pct <= threshold_pct:
+        return "OK"
+    if abs_delta_ns <= min_abs_ns:
+        return "NOISE"
+    return "FAIL"
+
+
+def render_markdown(rows: list[tuple[str, int, int, float, int]], threshold_pct: float, min_abs_ns: int) -> str:
     lines = [
         "## Benchmark Regression Report",
         "",
-        f"Threshold: {threshold_pct:.2f}%",
+        f"Thresholds: {threshold_pct:.2f}% and {min_abs_ns:,} ns absolute delta",
+        "",
+        "`NOISE` means the percentage threshold was exceeded, but the absolute delta was too small to fail CI.",
         "",
-        "| Tool | Base (ns) | Head (ns) | Delta | Status |",
-        "| --- | ---: | ---: | ---: | --- |",
+        "| Tool | Base (ns) | Head (ns) | Delta | Abs Delta (ns) | Status |",
+        "| --- | ---: | ---: | ---: | ---: | --- |",
     ]
-    for tool, base_ns, head_ns, delta in rows:
-        status = "FAIL" if delta > threshold_pct else "OK"
-        lines.append(f"| `{tool}` | {base_ns} | {head_ns} | {delta:+.2f}% | {status} |")
+    for tool, base_ns, head_ns, delta, abs_delta in rows:
+        status = status_for(delta, abs_delta, threshold_pct, min_abs_ns)
+        lines.append(f"| `{tool}` | {base_ns} | {head_ns} | {delta:+.2f}% | {abs_delta:+d} | {status} |")
     return "\n".join(lines) + "\n"
 
 
@@ -57,21 +67,21 @@ def main() -> int:
         return 1
     common = sorted(set(base) & set(head))
 
-    rows: list[tuple[str, int, int, float]] = []
+    rows: list[tuple[str, int, int, float, int]] = []
     failures: list[str] = []
 
     for tool in common:
         base_ns = int(base[tool]["avg_latency_ns"])
         head_ns = int(head[tool]["avg_latency_ns"])
         delta = pct_change(base_ns, head_ns)
         abs_delta = head_ns - base_ns
-        rows.append((tool, base_ns, head_ns, delta))
+        rows.append((tool, base_ns, head_ns, delta, abs_delta))
         # Only flag as regression if BOTH percentage AND absolute delta exceed thresholds
         # This prevents false positives on fast tools where CI noise dominates
         if delta > args.threshold_pct and abs_delta > args.min_abs_ns:
-            failures.append(f"{tool} regressed by {delta:.2f}%")
+            failures.append(f"{tool} regressed by {delta:.2f}% ({abs_delta:+d} ns)")
 
-    report = render_markdown(rows, args.threshold_pct)
+    report = render_markdown(rows, args.threshold_pct, args.min_abs_ns)
     sys.stdout.write(report)
 
     if args.markdown_out:

scripts/test_compare_bench.py

@@ -0,0 +1,35 @@
+#!/usr/bin/env python3
+from __future__ import annotations
+
+import importlib.util
+from pathlib import Path
+import unittest
+
+
+SCRIPT = Path(__file__).with_name("compare-bench.py")
+spec = importlib.util.spec_from_file_location("compare_bench", SCRIPT)
+assert spec is not None
+compare_bench = importlib.util.module_from_spec(spec)
+assert spec.loader is not None
+spec.loader.exec_module(compare_bench)
+
+
+class CompareBenchTests(unittest.TestCase):
+    def test_small_absolute_regression_is_noise(self) -> None:
+        self.assertEqual(compare_bench.status_for(22.54, 11_399, 10.0, 50_000), "NOISE")
+
+    def test_large_absolute_regression_fails(self) -> None:
+        self.assertEqual(compare_bench.status_for(12.0, 75_000, 10.0, 50_000), "FAIL")
+
+    def test_report_explains_noise_status(self) -> None:
+        report = compare_bench.render_markdown(
+            [("codedb_read", 50_580, 61_979, 22.54, 11_399)],
+            10.0,
+            50_000,
+        )
+        self.assertIn("50,000 ns absolute delta", report)
+        self.assertIn("| `codedb_read` | 50580 | 61979 | +22.54% | +11399 | NOISE |", report)
+
+
+if __name__ == "__main__":
+    unittest.main()