Address review feedback: fix hardcoded paths, PATH logic, SQLite mode

1. Replace all hardcoded /Users/whitenoise-oc/ dev paths in SEACLIP.md
   and TEST.md files (seaclip, pm2, chromadb) with generic placeholders
2. Extract shared _EXTRA_PATH_DIRS constant and _augmented_path() helper
   in pm2_backend.py so _find_pm2() and _build_env() use identical logic
3. Open SQLite in read-only mode (file:...?mode=ro) in _query_db()
4. Add trailing newline to registry.json

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

chromadb/agent-harness/cli_anything/chromadb/tests/TEST.md

@@ -63,11 +63,7 @@ Skipped:
 ## Running Tests
 
 ```bash
-# Activate the CLI-Anything venv
-source /Users/whitenoise-oc/projects/CLI-Anything/.venv/bin/activate
-
-# Install the package in dev mode
-cd /Users/whitenoise-oc/projects/cli-anything-chromadb/agent-harness
+cd agent-harness
 pip install -e .
 
 # Run all tests

pm2/agent-harness/cli_anything/pm2/tests/TEST.md

@@ -12,9 +12,8 @@ Test suites for the PM2 CLI-Anything harness.
 ## Running Tests
 
 ```bash
-# Activate the CLI-Anything venv
-source /Users/whitenoise-oc/projects/CLI-Anything/.venv/bin/activate
-cd /Users/whitenoise-oc/projects/cli-anything-pm2/agent-harness
+cd agent-harness
+pip install -e .
 
 # All tests
 python -m pytest cli_anything/pm2/tests/ -v

pm2/agent-harness/cli_anything/pm2/utils/pm2_backend.py

@@ -10,6 +10,18 @@ import shutil
 import subprocess
 from typing import Any
 
+# Common directories where pm2 may be installed (Homebrew, global npm, system).
+_EXTRA_PATH_DIRS = ["/opt/homebrew/bin", "/usr/local/bin", "/usr/bin"]
+
+
+def _augmented_path(base_path: str | None = None) -> str:
+    """Return PATH string with _EXTRA_PATH_DIRS prepended if missing."""
+    path = base_path if base_path is not None else os.environ.get("PATH", "")
+    for p in _EXTRA_PATH_DIRS:
+        if p not in path:
+            path = f"{p}:{path}"
+    return path
+
 
 def _find_pm2() -> str:
     """Locate the pm2 binary on the system.
@@ -22,13 +34,7 @@ def _find_pm2() -> str:
     Raises:
         RuntimeError: If pm2 is not found.
     """
-    extra_paths = ["/opt/homebrew/bin", "/usr/local/bin", "/usr/bin"]
-    env_path = os.environ.get("PATH", "")
-    for p in extra_paths:
-        if p not in env_path:
-            env_path = f"{p}:{env_path}"
-
-    pm2_path = shutil.which("pm2", path=env_path)
+    pm2_path = shutil.which("pm2", path=_augmented_path())
     if pm2_path is None:
         raise RuntimeError(
             "pm2 not found on this system. "
@@ -52,9 +58,7 @@ def _get_pm2() -> str:
 def _build_env() -> dict[str, str]:
     """Build environment dict with proper PATH for subprocess."""
     env = os.environ.copy()
-    extra = "/opt/homebrew/bin:/usr/local/bin"
-    if extra not in env.get("PATH", ""):
-        env["PATH"] = f"{extra}:{env.get('PATH', '')}"
+    env["PATH"] = _augmented_path(env.get("PATH", ""))
     return env
 
 

registry.json

@@ -538,4 +538,4 @@
       "contributor_url": "https://github.com/omerarslan0"
     }
   ]
-}
+}

seaclip/agent-harness/SEACLIP.md

@@ -30,7 +30,7 @@ or undo/redo stack.
 ## Backend
 
 - **FastAPI** at `http://127.0.0.1:5200`
-- **SQLite** at `/Users/whitenoise-oc/shrirama/seaclip-lite/seaclip.db`
+- **SQLite** at the path specified by the `SEACLIP_DB` environment variable
 
 ## Install
 
@@ -120,7 +120,7 @@ cli-anything-seaclip
 
 ```bash
 cd agent-harness
-source /Users/whitenoise-oc/projects/CLI-Anything/.venv/bin/activate
+pip install -e .
 python -m pytest cli_anything/seaclip/tests/ -v
 ```
 

seaclip/agent-harness/cli_anything/seaclip/tests/TEST.md

@@ -69,7 +69,6 @@ Tests requiring the live backend are skipped gracefully if localhost:5200 is unr
 ```
 ============================= test session starts ==============================
 platform darwin -- Python 3.14.3, pytest-9.0.2, pluggy-1.6.0
-rootdir: /Users/whitenoise-oc/projects/cli-anything-seaclip/agent-harness
 
 test_core.py     25 passed
 test_full_e2e.py 10 passed

seaclip/agent-harness/cli_anything/seaclip/utils/seaclip_backend.py

@@ -96,7 +96,7 @@ class SeaClipBackend:
                 "SEACLIP_DB environment variable is required for direct database queries. "
                 "Set it to the path of your SeaClip-Lite seaclip.db file."
             )
-        conn = sqlite3.connect(self.db_path)
+        conn = sqlite3.connect(f"file:{self.db_path}?mode=ro", uri=True)
         conn.row_factory = sqlite3.Row
         try:
             rows = conn.execute(sql, params).fetchall()