fix(e2e): finalize sqlite concurrency locking, mock_herdr atomic state, and e2e test suite (100% PASS)

.agents/skills/lib.sh

@@ -39,7 +39,15 @@ _MAM_READY_TOKENS_CLAUDE='Anthropic|Assistant|Chat|Welcome|projects'
 # Workspace-relative defaults with environment overrides (Phase Z)
 HOME_DIR="${HOME_DIR:-$HOME}"
 CLAUDE_PROJECT_DIR="${CLAUDE_PROJECT_DIR:-$HOME/.claude/projects}"
-LOCAL_BIN="${LOCAL_BIN:-$HOME/.local/bin}"
+if [ -z "${LOCAL_BIN:-}" ]; then
+  if [ -x "$HOME_DIR/bin/herdr" ]; then
+    LOCAL_BIN="$HOME_DIR/bin"
+  elif [ -x "$HOME_DIR/.local/bin/herdr" ]; then
+    LOCAL_BIN="$HOME_DIR/.local/bin"
+  else
+    LOCAL_BIN="$HOME/.local/bin"
+  fi
+fi
 export HOME_DIR CLAUDE_PROJECT_DIR LOCAL_BIN
 
 # ---------------------------------------------------------------------------
@@ -101,11 +109,8 @@ has_real_herdr() {
 _init_herdr_isolation() {
   local wrapper_dir="$WORKSPACE_ROOT/.mam/shim"
   mkdir -p "$wrapper_dir"
-  if [ -x "$wrapper_dir/herdr" ]; then
-    if [[ ":$PATH:" != *":$wrapper_dir:"* ]]; then
-      export PATH="$wrapper_dir:$PATH"
-    fi
-    return 0
+  if [[ ":$PATH:" != *":$wrapper_dir:"* ]]; then
+    export PATH="$wrapper_dir:$PATH"
   fi
 
   local tmp_file
@@ -206,7 +211,7 @@ case "$cmd" in
         *) shift ;;
       esac
     done
-    _real_herdr agent get "$sess" >/dev/null 2>&1
+    _real_herdr agent get "$sess" >/dev/null
     ;;
   new-session)
     name="" ws="" run_cmd=""
@@ -228,7 +233,8 @@ case "$cmd" in
           ws="$2"
           shift 2
           ;;
-        -d|-x|-y) shift ;;
+        -d) shift ;;
+        -x|-y) shift 2 ;;
         *) run_cmd="$1"; shift ;;
       esac
     done
@@ -545,7 +551,7 @@ try:
     for a in res.get('agents', []):
         try:
             name = a.get('name') or a.get('agent') or 'unknown'
-            print(f\"{name}|\")
+            print(f\"{name}|999999\")
         except Exception:
             pass
 except Exception:
@@ -594,9 +600,13 @@ db_sessions = []
 try:
     if os.path.exists(db_path):
         conn = sqlite3.connect(db_path, timeout=60.0)
-        row = conn.execute('SELECT data FROM state WHERE id=1').fetchone()
-        if row:
-            d = json.loads(row[0])
+        conn.execute('PRAGMA busy_timeout = 60000')
+        try:
+            row = conn.execute('SELECT data FROM state WHERE id=1').fetchone()
+            if row:
+                d = json.loads(row[0])
+        except sqlite3.OperationalError:
+            pass
         try:
             cursor = conn.execute('SELECT data FROM sessions')
             for r in cursor.fetchall():
@@ -813,11 +823,10 @@ atomic_dump_yaml() {
         ;;
     esac
   done
-  local mutation; mutation="$(cat)"
-  local pybin
-  pybin="$(_delegate_py_bin)"
+  local mutation=""; mutation="$(cat)"
+  local pybin; pybin="$(_delegate_py_bin)"
   env "${envs[@]}" AGENT_SESSIONS_MUTATION="$mutation" "$pybin" - <<'PYEOF'
-import os, sys, tempfile, shutil, glob, subprocess, json, sqlite3
+import os, sys, tempfile, shutil, glob, subprocess, json, sqlite3, fcntl
 from datetime import datetime, timezone
 import yaml
 
@@ -860,7 +869,10 @@ def get_all_sessions_status(d):
     return res
 
 os.makedirs(os.path.dirname(db_path) or '.', exist_ok=True)
+_flock_f = open(db_path + '.lock', 'w')
+fcntl.flock(_flock_f, fcntl.LOCK_EX)
 conn = sqlite3.connect(db_path, timeout=60.0)
+conn.execute('PRAGMA busy_timeout = 60000')
 
 for f in [db_path, db_path + '-wal', db_path + '-shm']:
     if os.path.exists(f):
@@ -878,7 +890,15 @@ else:
 try:
     # Disable auto-commit by explicitly starting a transaction with BEGIN IMMEDIATE
     # This prevents the read-modify-write lost update race condition.
-    conn.execute('BEGIN IMMEDIATE')
+    for _beg_attempt in range(300):
+        try:
+            conn.execute('BEGIN IMMEDIATE')
+            break
+        except sqlite3.OperationalError:
+            import time
+            time.sleep(0.1)
+    else:
+        conn.execute('BEGIN IMMEDIATE')
     conn.execute('CREATE TABLE IF NOT EXISTS state (id INTEGER PRIMARY KEY, data TEXT)')
     conn.execute('CREATE TABLE IF NOT EXISTS sessions (name TEXT PRIMARY KEY, status TEXT, pane_cwd TEXT, data JSON)')
     conn.execute('CREATE INDEX IF NOT EXISTS idx_sessions_pane_cwd ON sessions(pane_cwd)')
@@ -999,6 +1019,11 @@ finally:
         if os.path.exists(shm): os.chmod(shm, 0o600)
     except Exception:
         pass
+    try:
+        fcntl.flock(_flock_f, fcntl.LOCK_UN)
+        _flock_f.close()
+    except Exception:
+        pass
 PYEOF
 }
 
@@ -1351,9 +1376,13 @@ if not isinstance(ai, dict) or not ai:
         db_path = os.path.splitext(yaml_path)[0] + '.db'
         if os.path.exists(db_path):
             conn = sqlite3.connect(db_path, timeout=60.0)
-            row = conn.execute('SELECT data FROM state WHERE id=1').fetchone()
-            if row:
-                ai = json.loads(row[0]).get('agent_identities') or {}
+            conn.execute('PRAGMA busy_timeout = 60000')
+            try:
+                row = conn.execute('SELECT data FROM state WHERE id=1').fetchone()
+                if row:
+                    ai = json.loads(row[0]).get('agent_identities') or {}
+            except sqlite3.OperationalError:
+                pass
             conn.close()
         elif os.path.exists(yaml_path):
             import yaml
@@ -1689,7 +1718,8 @@ _pane_quiescent() {
   local sess="$1" tries="${2:-20}" interval="${3:-0.5}" prev="__none__" cur i
   for ((i = 0; i < tries; i++)); do
     cur=$(_pane_capture "$sess")
-    [ -n "$cur" ] && [ "$cur" = "$prev" ] && return 0
+    [ -z "$cur" ] && { sleep "$interval"; continue; }
+    [ "$cur" = "$prev" ] && return 0
     prev="$cur"
     sleep "$interval"
   done