nexo-brain 5.3.28 → 5.3.30

package/.claude-plugin/plugin.json

@@ -1,6 +1,6 @@
 {
   "name": "nexo-brain",
-  "version": "5.3.28",
+  "version": "5.3.30",
   "description": "Local cognitive runtime for Claude Code \u2014 persistent memory, overnight learning, doctor diagnostics, personal scripts, recovery-aware jobs, startup preflight, and optional dashboard/power helper.",
   "author": {
     "name": "NEXO Brain",

package/README.md

@@ -18,7 +18,9 @@
 
 [Watch the overview video](https://nexo-brain.com/watch/) · [Watch on YouTube](https://www.youtube.com/watch?v=i2lkGhKyVqI) · [Open the infographic](https://nexo-brain.com/assets/nexo-brain-infographic-v5.png)
 
-Version `5.3.11` is the current packaged-runtime line: protocol and Cortex now reject malformed `outcome`, `task_type`, and `impact_level` values explicitly instead of silently coercing them into other valid states, so task history, debt, hot context, and decision telemetry stay trustworthy even when a caller passes a bad contract payload.
+Version `5.3.30` is the current packaged-runtime line: four read-only CLI commands (`nexo schema`, `nexo identity`, `nexo onboard`, `nexo scan-profile`) let external UIs like NEXO Desktop auto-adapt to the editable schema, canonical identity, onboarding wizard, and profile heuristics without hardcoding fields.
+
+Previously in `5.3.29`: duplicate `* 2` artifacts now fail hygiene gates instead of hiding in the tree, packaged/runtime update paths converge on one canonical core, startup preflight runs synchronously, corrupt DB state no longer respawns an empty brain by default, and cron runs spool locally when SQLite is unavailable.
 
 Start here:
 - [5-minute quickstart](docs/quickstart-5-minutes.md)
@@ -488,7 +490,9 @@ NEXO Brain doesn't just respond — it runs 13 core recovery-aware background jo
 | **followup-hygiene** | Weekly (Sun) | Normalizes statuses, flags stale followups, cleans orphans |
 | **learning-housekeep** | 03:15 daily | Dedup learnings, adjust weights by usage, process overdue reviews, reconcile decision outcomes |
 | **immune** | Every 30 min | Quarantine processing, memory promotion/rejection, synaptic pruning |
+| **impact-scorer** | 05:45 daily | Scores active followups so queues can prioritize by expected impact |
 | **synthesis** | 06:00 daily | Memory synthesis — discovers cross-memory patterns |
+| **outcome-checker** | 08:00 daily | Verifies tracked outcomes and marks them met, pending, or missed |
 | **watchdog** | Every 30 min | Monitors services, LaunchAgents, and infrastructure health |
 | **auto-close-sessions** | Every 5 min | Cleans stale sessions |
 

package/bin/nexo-brain.js

@@ -88,6 +88,20 @@ function log(msg) {
   console.log(`  ${msg}`);
 }
 
+function duplicateArtifactCanonicalName(name) {
+  const ext = path.extname(name);
+  const stem = ext ? name.slice(0, -ext.length) : name;
+  const match = stem.match(/^(.*) ([2-9]\d*)$/);
+  if (!match) return null;
+  return `${match[1]}${ext}`;
+}
+
+function isDuplicateArtifactName(name, dirPath = "") {
+  const canonical = duplicateArtifactCanonicalName(name);
+  if (!canonical || !dirPath) return false;
+  return fs.existsSync(path.join(dirPath, canonical));
+}
+
 function syncWatchdogHashRegistry(nexoHome) {
   try {
     const watchdogPath = path.join(nexoHome, "scripts", "nexo-watchdog.sh");
@@ -122,7 +136,7 @@ function writeRuntimeCoreArtifactsManifest(nexoHome, srcDir) {
       return fs.readdirSync(dirPath)
         .filter((name) => {
           const full = path.join(dirPath, name);
-          return fs.existsSync(full) && fs.statSync(full).isFile();
+          return fs.existsSync(full) && fs.statSync(full).isFile() && !isDuplicateArtifactName(name, dirPath);
         })
         .sort();
     };
@@ -192,6 +206,7 @@ function getCoreRuntimeFlatFiles(srcDir = path.join(__dirname, "..", "src")) {
   const discoveredRootModules = fs.existsSync(srcDir)
     ? fs.readdirSync(srcDir)
       .filter((name) => {
+        if (isDuplicateArtifactName(name, srcDir)) return false;
         const stat = fs.statSync(path.join(srcDir, name));
         if (!stat.isFile()) return false;
         // Include Python modules and any flat JSON config the Python runtime
@@ -1551,7 +1566,7 @@ async function main() {
         const copyDirRec = (src, dest) => {
           fs.mkdirSync(dest, { recursive: true });
           fs.readdirSync(src).forEach(item => {
-            if (item === "__pycache__" || item.endsWith(".pyc") || item.endsWith(".db")) return;
+            if (item === "__pycache__" || item.endsWith(".pyc") || item.endsWith(".db") || isDuplicateArtifactName(item, src)) return;
             const srcPath = path.join(src, item);
             const destPath = path.join(dest, item);
             if (fs.statSync(srcPath).isDirectory()) {
@@ -1620,7 +1635,7 @@ async function main() {
         const pluginsDest = path.join(NEXO_HOME, "plugins");
         fs.mkdirSync(pluginsDest, { recursive: true });
         if (fs.existsSync(pluginsSrc)) {
-          fs.readdirSync(pluginsSrc).filter(f => f.endsWith(".py")).forEach((f) => {
+          fs.readdirSync(pluginsSrc).filter(f => f.endsWith(".py") && !isDuplicateArtifactName(f, pluginsSrc)).forEach((f) => {
             fs.copyFileSync(path.join(pluginsSrc, f), path.join(pluginsDest, f));
           });
         }
@@ -1772,7 +1787,7 @@ async function main() {
         const copyDirRec2 = (src, dest) => {
           fs.mkdirSync(dest, { recursive: true });
           fs.readdirSync(src).forEach(item => {
-            if (item === "__pycache__" || item.endsWith(".pyc") || item.endsWith(".db")) return;
+            if (item === "__pycache__" || item.endsWith(".pyc") || item.endsWith(".db") || isDuplicateArtifactName(item, src)) return;
             const srcP = path.join(src, item);
             const destP = path.join(dest, item);
             if (fs.statSync(srcP).isDirectory()) copyDirRec2(srcP, destP);
@@ -1806,7 +1821,7 @@ async function main() {
         const copyDirRec3 = (src, dest) => {
           fs.mkdirSync(dest, { recursive: true });
           fs.readdirSync(src).forEach(item => {
-            if (item === "__pycache__" || item.endsWith(".pyc")) return;
+            if (item === "__pycache__" || item.endsWith(".pyc") || isDuplicateArtifactName(item, src)) return;
             const srcP = path.join(src, item);
             const destP = path.join(dest, item);
             if (fs.statSync(srcP).isDirectory()) copyDirRec3(srcP, destP);
@@ -1831,6 +1846,7 @@ async function main() {
       if (fs.existsSync(templatesSrc)) {
         fs.mkdirSync(templatesDest, { recursive: true });
         for (const f of fs.readdirSync(templatesSrc)) {
+          if (isDuplicateArtifactName(f, templatesSrc)) continue;
           const src = path.join(templatesSrc, f);
           const dest = path.join(templatesDest, f);
           if (fs.statSync(src).isFile()) {
@@ -1838,6 +1854,7 @@ async function main() {
           } else if (fs.statSync(src).isDirectory()) {
             fs.mkdirSync(dest, { recursive: true });
             for (const sf of fs.readdirSync(src)) {
+              if (isDuplicateArtifactName(sf, src)) continue;
               const ssrc = path.join(src, sf);
               if (fs.statSync(ssrc).isFile()) {
                 fs.copyFileSync(ssrc, path.join(dest, sf));
@@ -2354,7 +2371,7 @@ async function main() {
   const copyDirRecursive = (src, dest) => {
     fs.mkdirSync(dest, { recursive: true });
     fs.readdirSync(src).forEach(item => {
-      if (item === "__pycache__" || item.endsWith(".pyc") || item.endsWith(".db")) return;
+      if (item === "__pycache__" || item.endsWith(".pyc") || item.endsWith(".db") || isDuplicateArtifactName(item, src)) return;
       const srcPath = path.join(src, item);
       const destPath = path.join(dest, item);
       if (fs.statSync(srcPath).isDirectory()) {
@@ -2461,7 +2478,7 @@ async function main() {
   // Plugins (all .py files in plugins/)
   fs.mkdirSync(path.join(NEXO_HOME, "plugins"), { recursive: true });
   if (fs.existsSync(pluginsSrcDir)) {
-    fs.readdirSync(pluginsSrcDir).filter(f => f.endsWith(".py")).forEach((f) => {
+    fs.readdirSync(pluginsSrcDir).filter(f => f.endsWith(".py") && !isDuplicateArtifactName(f, pluginsSrcDir)).forEach((f) => {
       fs.copyFileSync(path.join(pluginsSrcDir, f), path.join(NEXO_HOME, "plugins", f));
     });
   }

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "nexo-brain",
-  "version": "5.3.28",
+  "version": "5.3.30",
   "mcpName": "io.github.wazionapps/nexo",
   "description": "NEXO Brain — Shared brain for AI agents. Persistent memory, semantic RAG, natural forgetting, metacognitive guard, trust scoring, 150+ MCP tools. Works with Claude Code, Codex, Claude Desktop & any MCP client. 100% local, free.",
   "homepage": "https://nexo-brain.com",

package/src/auto_update.py

@@ -18,6 +18,7 @@ import time
 from pathlib import Path
 
 from runtime_home import export_resolved_nexo_home, managed_nexo_home
+from tree_hygiene import is_duplicate_artifact_name
 
 NEXO_HOME = export_resolved_nexo_home()
 DATA_DIR = NEXO_HOME / "data"
@@ -63,6 +64,20 @@ def _log(msg: str):
     print(f"[NEXO auto-update] {msg}", file=sys.stderr)
 
 
+def _runtime_copy_ignore(*extra_patterns: str):
+    base_ignore = shutil.ignore_patterns("__pycache__", "*.pyc", "*.pyo", "*.db", *extra_patterns)
+
+    def _ignore(dir_name: str, names: list[str]) -> set[str]:
+        ignored = set(base_ignore(dir_name, names))
+        ignored.update(
+            name for name in names
+            if is_duplicate_artifact_name(Path(dir_name) / name)
+        )
+        return ignored
+
+    return _ignore
+
+
 def _critical_table_count(db_path: Path, table: str) -> int | None:
     """Return COUNT(*) for a critical table when it exists, otherwise None."""
     import sqlite3
@@ -470,7 +485,7 @@ def _refresh_installed_manifest():
         if src_crons.exists():
             dst_crons.mkdir(parents=True, exist_ok=True)
             for f in src_crons.iterdir():
-                if f.is_file():
+                if f.is_file() and not is_duplicate_artifact_name(f):
                     shutil.copy2(str(f), str(dst_crons / f.name))
             _log("Refreshed installed crons manifest")
     except Exception as e:
@@ -746,7 +761,7 @@ def _sync_hooks():
     hooks_dest.mkdir(parents=True, exist_ok=True)
     synced = 0
     for f in hooks_src.iterdir():
-        if f.is_file() and f.suffix == ".sh":
+        if f.is_file() and f.suffix == ".sh" and not is_duplicate_artifact_name(f):
             dest = hooks_dest / f.name
             shutil.copy2(str(f), str(dest))
             os.chmod(str(dest), 0o755)
@@ -1441,7 +1456,7 @@ def _auto_update_check_locked() -> dict:
             import shutil
             scripts_dest.mkdir(parents=True, exist_ok=True)
             for f in scripts_src.iterdir():
-                if f.name.startswith('.') or f.name == '__pycache__':
+                if f.name.startswith('.') or f.name == '__pycache__' or is_duplicate_artifact_name(f):
                     continue
                 dest = scripts_dest / f.name
                 if f.is_file() and not dest.exists():
@@ -1475,12 +1490,12 @@ def _auto_update_check_locked() -> dict:
         if doctor_src.is_dir():
             import shutil
             if not doctor_dest.is_dir():
-                shutil.copytree(str(doctor_src), str(doctor_dest), ignore=shutil.ignore_patterns("__pycache__", "*.pyc"))
+                shutil.copytree(str(doctor_src), str(doctor_dest), ignore=_runtime_copy_ignore())
                 _log("Backfilled doctor package")
             else:
                 # Update existing files
                 for root, dirs, files in os.walk(str(doctor_src)):
-                    dirs[:] = [d for d in dirs if d != "__pycache__"]
+                    dirs[:] = [d for d in dirs if d != "__pycache__" and not is_duplicate_artifact_name(Path(root) / d)]
                     rel = os.path.relpath(root, str(doctor_src))
                     dest_dir = doctor_dest / rel
                     dest_dir.mkdir(parents=True, exist_ok=True)
@@ -1488,6 +1503,8 @@ def _auto_update_check_locked() -> dict:
                         if f.endswith(".pyc"):
                             continue
                         src_f = Path(root) / f
+                        if is_duplicate_artifact_name(src_f):
+                            continue
                         dst_f = dest_dir / f
                         if not dst_f.exists() or src_f.stat().st_mtime > dst_f.stat().st_mtime:
                             shutil.copy2(str(src_f), str(dst_f))
@@ -1501,11 +1518,11 @@ def _auto_update_check_locked() -> dict:
         if skills_src.is_dir():
             import shutil
             if not skills_dest.is_dir():
-                shutil.copytree(str(skills_src), str(skills_dest), ignore=shutil.ignore_patterns("__pycache__", "*.pyc"))
+                shutil.copytree(str(skills_src), str(skills_dest), ignore=_runtime_copy_ignore())
                 _log("Backfilled skills-core")
             else:
                 for root, dirs, files in os.walk(str(skills_src)):
-                    dirs[:] = [d for d in dirs if d != "__pycache__"]
+                    dirs[:] = [d for d in dirs if d != "__pycache__" and not is_duplicate_artifact_name(Path(root) / d)]
                     rel = os.path.relpath(root, str(skills_src))
                     dest_dir = skills_dest / rel
                     dest_dir.mkdir(parents=True, exist_ok=True)
@@ -1513,6 +1530,8 @@ def _auto_update_check_locked() -> dict:
                         if f.endswith(".pyc"):
                             continue
                         src_f = Path(root) / f
+                        if is_duplicate_artifact_name(src_f):
+                            continue
                         dst_f = dest_dir / f
                         if not dst_f.exists() or src_f.stat().st_mtime > dst_f.stat().st_mtime:
                             shutil.copy2(str(src_f), str(dst_f))
@@ -1539,7 +1558,7 @@ def _auto_update_check_locked() -> dict:
         import shutil
         if templates_src.is_dir():
             for item in templates_src.iterdir():
-                if item.name == "__pycache__":
+                if item.name == "__pycache__" or is_duplicate_artifact_name(item):
                     continue
                 dest_item = templates_dest / item.name
                 if item.is_file():
@@ -1548,7 +1567,7 @@ def _auto_update_check_locked() -> dict:
                 elif item.is_dir():
                     dest_item.mkdir(parents=True, exist_ok=True)
                     for sub in item.iterdir():
-                        if sub.is_file():
+                        if sub.is_file() and not is_duplicate_artifact_name(sub):
                             dest_sub = dest_item / sub.name
                             if not dest_sub.exists() or sub.stat().st_mtime > dest_sub.stat().st_mtime:
                                 shutil.copy2(str(sub), str(dest_sub))
@@ -1735,6 +1754,8 @@ def _discover_runtime_root_python_modules(base_dir: Path) -> list[str]:
             continue
         if item.name.startswith(".") or item.name == "__init__.py":
             continue
+        if is_duplicate_artifact_name(item):
+            continue
         modules.append(item.name)
     return modules
 
@@ -1857,7 +1878,7 @@ def _copy_runtime_from_source(src_dir: Path, repo_dir: Path, dest: Path = NEXO_H
             shutil.copytree(
                 str(pkg_src),
                 str(pkg_dest),
-                ignore=shutil.ignore_patterns("__pycache__", "*.pyc", "*.pyo", "*.db"),
+                ignore=_runtime_copy_ignore(),
             )
             copied_packages += 1
 
@@ -1874,7 +1895,7 @@ def _copy_runtime_from_source(src_dir: Path, repo_dir: Path, dest: Path = NEXO_H
     if plugins_src.is_dir():
         plugins_dest.mkdir(parents=True, exist_ok=True)
         for item in plugins_src.iterdir():
-            if item.is_file() and item.suffix == ".py":
+            if item.is_file() and item.suffix == ".py" and not is_duplicate_artifact_name(item):
                 shutil.copy2(str(item), str(plugins_dest / item.name))
 
     _emit_progress(progress_fn, "Copying scripts...")
@@ -1883,13 +1904,13 @@ def _copy_runtime_from_source(src_dir: Path, repo_dir: Path, dest: Path = NEXO_H
     if scripts_src.is_dir():
         scripts_dest.mkdir(parents=True, exist_ok=True)
         for item in scripts_src.iterdir():
-            if item.name == "__pycache__" or item.name.startswith("."):
+            if item.name == "__pycache__" or item.name.startswith(".") or is_duplicate_artifact_name(item):
                 continue
             dst = scripts_dest / item.name
             if item.is_dir():
                 if dst.exists():
                     shutil.rmtree(str(dst), ignore_errors=True)
-                shutil.copytree(str(item), str(dst), ignore=shutil.ignore_patterns("__pycache__", "*.pyc"))
+                shutil.copytree(str(item), str(dst), ignore=_runtime_copy_ignore())
             elif item.is_file():
                 existing_class = installed_script_classes.get(item.name, "")
                 if dst.exists() and existing_class in {"personal", "non-script"}:
@@ -1919,7 +1940,7 @@ def _copy_runtime_from_source(src_dir: Path, repo_dir: Path, dest: Path = NEXO_H
     if templates_src.is_dir():
         templates_dest.mkdir(parents=True, exist_ok=True)
         for item in templates_src.iterdir():
-            if item.name == "__pycache__":
+            if item.name == "__pycache__" or is_duplicate_artifact_name(item):
                 continue
             if item.is_file():
                 shutil.copy2(str(item), str(templates_dest / item.name))
@@ -1927,7 +1948,7 @@ def _copy_runtime_from_source(src_dir: Path, repo_dir: Path, dest: Path = NEXO_H
                 sub_dest = templates_dest / item.name
                 sub_dest.mkdir(parents=True, exist_ok=True)
                 for sub in item.iterdir():
-                    if sub.is_file():
+                    if sub.is_file() and not is_duplicate_artifact_name(sub):
                         shutil.copy2(str(sub), str(sub_dest / sub.name))
 
     package_json = repo_dir / "package.json"
@@ -1948,7 +1969,7 @@ def _copy_runtime_from_source(src_dir: Path, repo_dir: Path, dest: Path = NEXO_H
     if skills_src.is_dir():
         if skills_dest.exists():
             shutil.rmtree(str(skills_dest), ignore_errors=True)
-        shutil.copytree(str(skills_src), str(skills_dest), ignore=shutil.ignore_patterns("__pycache__", "*.pyc"))
+        shutil.copytree(str(skills_src), str(skills_dest), ignore=_runtime_copy_ignore())
 
     bin_dir = dest / "bin"
     bin_dir.mkdir(parents=True, exist_ok=True)

package/src/cli.py

@@ -1944,6 +1944,21 @@ def main():
     dashboard_parser = sub.add_parser("dashboard", help="Web dashboard control")
     dashboard_parser.add_argument("action", choices=["on", "off", "status"], help="Start, stop, or check dashboard")
 
+    # -- desktop bridge (read-only, for NEXO Desktop and any external UI) --
+    schema_parser = sub.add_parser("schema", help="Editable-field schema for Preferences UI")
+    schema_parser.add_argument("--json", action="store_true", help="JSON output (default)")
+
+    identity_parser = sub.add_parser("identity", help="Canonical assistant identity")
+    identity_parser.add_argument("--json", action="store_true", help="JSON output (default)")
+
+    onboard_parser = sub.add_parser("onboard", help="Onboarding wizard steps")
+    onboard_parser.add_argument("--json", action="store_true", help="JSON output (default)")
+
+    scan_profile_parser = sub.add_parser("scan-profile", help="Build profile.json from CLAUDE.md + calibration")
+    scan_profile_parser.add_argument("--json", action="store_true", help="JSON output")
+    scan_profile_parser.add_argument("--apply", action="store_true", help="Write profile.json (default is preview)")
+    scan_profile_parser.add_argument("--force", action="store_true", help="Overwrite existing profile.json on --apply")
+
     args = parser.parse_args()
 
     if args.help or (not args.command and not args.version):
@@ -2037,6 +2052,14 @@ def main():
         return _uninstall(args)
     elif args.command == "dashboard":
         return _dashboard(args)
+    elif args.command in ("schema", "identity", "onboard", "scan-profile"):
+        from desktop_bridge import cmd_schema, cmd_identity, cmd_onboard, cmd_scan_profile
+        return {
+            "schema": cmd_schema,
+            "identity": cmd_identity,
+            "onboard": cmd_onboard,
+            "scan-profile": cmd_scan_profile,
+        }[args.command](args)
     else:
         _print_help()
         return 0