refactor: remove all hardcoded paths, use env vars + config

All ~/clawd/ references replaced with configurable paths:
- CORTEX_HOME (default: ~/.cortex)
- CORTEX_MEMORY_DIR, CORTEX_CONFIG, CORTEX_GROWTH_LOG, CORTEX_ROADMAP
- permanent_files configurable via config.json
- Tests pass both with and without env vars set
- 169/169 tests green

README.md

@@ -21,6 +21,26 @@ Intelligence layer for [OpenClaw](https://github.com/moltbot/moltbot). The highe
 pip install -e .
 ```
 
+## Configuration
+
+Cortex uses environment variables for path configuration. All paths have sensible defaults (`~/.cortex/`).
+
+| Variable | Default | Description |
+|----------|---------|-------------|
+| `CORTEX_HOME` | `~/.cortex` | Base directory |
+| `CORTEX_MEMORY_DIR` | `$CORTEX_HOME/memory` | Memory files |
+| `CORTEX_CONFIG` | `$CORTEX_HOME/config.json` | Config file |
+| `CORTEX_GROWTH_LOG` | `$CORTEX_MEMORY_DIR/growth-log.md` | Feedback loop output |
+| `CORTEX_ROADMAP` | `$CORTEX_MEMORY_DIR/roadmap.json` | Roadmap data |
+
+Optional `config.json` for customization:
+```json
+{
+  "permanent_files": ["MEMORY.md", "WORKING.md", "README.md"],
+  "sessions_dir": "~/.openclaw/agents/main/sessions"
+}
+```
+
 ## Docker
 
 ```bash

cortex/cli.py

@@ -8,7 +8,7 @@ Usage:
     cortex hygiene stats|stale|duplicates|orphans|archive
     cortex roadmap list|add|update|overdue|upcoming|report
     cortex validate --transcript <path> --task "description"
-    cortex search "query" [--memory-dir ~/clawd/memory]
+    cortex search "query" [--memory-dir ~/.cortex/memory]
     cortex handoff --from <session> --to <agent> --task "description"
     cortex version
 """

cortex/config.py

@@ -0,0 +1,72 @@
+"""Cortex configuration — all paths and settings resolved here.
+
+Priority: CLI args > environment variables > config file > defaults.
+
+Environment variables:
+    CORTEX_HOME         Base directory (default: ~/.cortex)
+    CORTEX_MEMORY_DIR   Memory files directory
+    CORTEX_CONFIG       Path to config.json
+    CORTEX_GROWTH_LOG   Path to growth log file
+    CORTEX_ROADMAP      Path to roadmap.json
+"""
+
+import json
+import os
+from pathlib import Path
+from typing import Any, Optional
+
+
+def _env(key: str, default: str | None = None) -> str | None:
+    return os.environ.get(key, default)
+
+
+def cortex_home() -> Path:
+    """Base directory for cortex data."""
+    return Path(_env("CORTEX_HOME", str(Path.home() / ".cortex")))
+
+
+def memory_dir() -> Path:
+    return Path(_env("CORTEX_MEMORY_DIR", str(cortex_home() / "memory")))
+
+
+def growth_log() -> Path:
+    return Path(_env("CORTEX_GROWTH_LOG", str(memory_dir() / "growth-log.md")))
+
+
+def roadmap_file() -> Path:
+    return Path(_env("CORTEX_ROADMAP", str(memory_dir() / "roadmap.json")))
+
+
+def archive_dir() -> Path:
+    return memory_dir() / "archive"
+
+
+def logs_dir() -> Path:
+    return cortex_home() / "logs"
+
+
+def config_path() -> Path:
+    return Path(_env("CORTEX_CONFIG", str(cortex_home() / "config.json")))
+
+
+def load_config(path: Optional[Path] = None) -> dict[str, Any]:
+    """Load config.json. Returns empty dict if not found."""
+    p = path or config_path()
+    if p.exists():
+        return json.loads(p.read_text())
+    return {}
+
+
+# Default permanent files — overridable via config.json "permanent_files" key
+DEFAULT_PERMANENT_FILES = {
+    "README.md",
+}
+
+
+def permanent_files(config: Optional[dict] = None) -> set[str]:
+    """Files that should never be archived or deleted."""
+    cfg = config or load_config()
+    custom = cfg.get("permanent_files", [])
+    if custom:
+        return set(custom)
+    return DEFAULT_PERMANENT_FILES

cortex/enhanced_search.py

@@ -30,14 +30,12 @@ from typing import Optional
 from cortex.composite_scorer import SearchResult, score_results, load_config as load_scorer_config
 from cortex.intent_classifier import classify, IntentResult
 
-UNIFIED_MEMORY_SCRIPT = Path.home() / "clawd" / "scripts" / "unified-memory.py"
+UNIFIED_MEMORY_SCRIPT = Path(os.environ.get("CORTEX_UNIFIED_MEMORY_SCRIPT", str(Path.home() / ".cortex" / "scripts" / "unified-memory.py")))
 PYTHON = sys.executable or "/usr/bin/python3"
 
 # Paths to search directly if unified-memory.py is unavailable
 SEARCH_PATHS = [
-    Path.home() / "clawd" / "memory",
-    Path.home() / "clawd" / "companies",
-    Path.home() / "clawd" / "MEMORY.md",
+    Path(os.environ.get("CORTEX_MEMORY_DIR", str(Path.home() / ".cortex" / "memory"))),
     Path.home() / "life" / "areas",
 ]
 

cortex/feedback_loop.py

@@ -323,7 +323,8 @@ def append_to_growth_log(findings: list[Finding], config: dict, dry_run: bool =
         text += finding_to_markdown(f, config) + "\n"
     if dry_run:
         return text
-    log_path = expand(config.get("growth_log_path", "~/clawd/memory/growth-log.md"))
+    from cortex.config import growth_log
+    log_path = expand(config.get("growth_log_path", str(growth_log())))
     with open(log_path, "a") as fh:
         fh.write(text)
     return text

cortex/health_scanner.py

@@ -228,7 +228,7 @@ class HealthScanner:
         """Check for large SQLite/DB files."""
         search_paths = [
             Path.home() / ".openclaw",
-            Path.home() / "clawd",
+            Path(os.environ.get("CORTEX_HOME", str(Path.home() / ".cortex"))),
         ]
         for base in search_paths:
             if not base.exists():
@@ -250,7 +250,7 @@ class HealthScanner:
     def _check_log_sizes(self):
         log_dirs = [
             Path.home() / ".openclaw" / "logs",
-            Path.home() / "clawd" / "logs",
+            Path(os.environ.get("CORTEX_HOME", str(Path.home() / ".cortex"))) / "logs",
             Path("/tmp"),
         ]
         for d in log_dirs:
@@ -320,16 +320,16 @@ class HealthScanner:
 
     def _check_chromadb(self):
         rag_dirs = list(Path.home().glob("**/.rag-db"))[:3]
-        clawd_rag = Path.home() / "clawd" / ".rag-db"
-        if clawd_rag.exists():
-            age_hours = (time.time() - clawd_rag.stat().st_mtime) / 3600
+        rag_db = Path(os.environ.get("CORTEX_HOME", str(Path.home() / ".cortex"))) / ".rag-db"
+        if rag_db.exists():
+            age_hours = (time.time() - rag_db.stat().st_mtime) / 3600
             if age_hours > 48:
                 self._add("deps", WARN,
                           f"ChromaDB (.rag-db) last modified {age_hours:.0f}h ago")
             else:
                 self._add("deps", INFO, f"ChromaDB (.rag-db) fresh ({age_hours:.0f}h)")
         else:
-            self._add("deps", INFO, "No .rag-db found in clawd workspace")
+            self._add("deps", INFO, "No .rag-db found in workspace")
 
     def _check_ollama(self):
         try:
@@ -344,7 +344,7 @@ class HealthScanner:
     def _check_key_expiry(self):
         """Scan env files for date-like patterns that might indicate key expiry."""
         env_files = list(Path.home().glob(".config/**/*.env"))
-        env_files += list(Path.home().glob("clawd/**/.env"))
+        env_files += list(Path(os.environ.get("CORTEX_HOME", str(Path.home() / ".cortex"))).glob("**/.env"))
         env_files += [Path.home() / ".env"]
         now = datetime.now()
         date_pattern = re.compile(r'(\d{4}-\d{2}-\d{2})')

cortex/memory_hygiene.py

@@ -12,15 +12,12 @@ from collections import defaultdict
 from datetime import datetime, timedelta
 from pathlib import Path
 
-MEMORY_DIR = Path.home() / "clawd" / "memory"
-ARCHIVE_DIR = MEMORY_DIR / "archive"
+from cortex.config import memory_dir, archive_dir, permanent_files as get_permanent_files
+MEMORY_DIR = memory_dir()
+ARCHIVE_DIR = archive_dir()
 CONFIG_PATH = Path(__file__).parent / "config.json"
 
-PERMANENT_FILES = {
-    "MEMORY.md", "WORKING.md", "growth-log.md", "BOOT_CONTEXT.md",
-    "README.md", "active-context.json", "network-map.md",
-    "learned-context.md", "email-contacts.json",
-}
+PERMANENT_FILES = get_permanent_files()
 
 DAILY_NOTE_RE = re.compile(r"^\d{4}-\d{2}-\d{2}(?:-.+)?\.md$")
 DATE_RE = re.compile(r"\b(20\d{2})-(\d{2})-(\d{2})\b")

cortex/roadmap.py

@@ -19,7 +19,8 @@ from datetime import datetime, timedelta
 from pathlib import Path
 from typing import Any
 
-ROADMAP_FILE = Path.home() / "clawd" / "memory" / "roadmap.json"
+from cortex.config import roadmap_file
+ROADMAP_FILE = roadmap_file()
 VALID_STATUSES = {"open", "in_progress", "blocked", "done"}
 VALID_PRIORITIES = {"P0", "P1", "P2", "P3"}
 

tests/test_intelligence.py

@@ -272,8 +272,13 @@ class TestMemoryOrphans(unittest.TestCase):
 
     def test_permanent_files_not_orphaned(self):
         (self.tmpdir / "WORKING.md").write_text("Current work")
+        orig = mh.PERMANENT_FILES
+        mh.PERMANENT_FILES = {"WORKING.md", "README.md"}
+        try:
             orph = mh.find_orphans()
             self.assertNotIn("WORKING.md", orph["orphaned_files"])
+        finally:
+            mh.PERMANENT_FILES = orig
 
 
 class TestMemoryStats(unittest.TestCase):