merge: feat/wf5-securestorage into the 0.0.50 integration line

Brings the per-agent harness-home work (FLEET_SEAT) onto the release line.
Clean merge, no conflicts.

packages/mosaic/framework/tools/_scripts/mosaic-ensure-sequential-thinking

@@ -5,6 +5,7 @@ MOSAIC_HOME="${MOSAIC_HOME:-$HOME/.config/mosaic}"
 MODE="apply"
 RUNTIME="all"
 STRICT_CHECK=0
+CLAUDE_CONFIG_DIR=""
 
 PKG="@modelcontextprotocol/server-sequential-thinking"
 
@@ -29,6 +30,14 @@ while [[ $# -gt 0 ]]; do
       STRICT_CHECK=1
       shift
       ;;
+    --claude-config-dir)
+      if [[ $# -lt 2 ]]; then
+        err "--claude-config-dir requires an absolute seat config directory"
+        exit 2
+      fi
+      CLAUDE_CONFIG_DIR="$2"
+      shift 2
+      ;;
     *)
       err "Unknown argument: $1"
       exit 2
@@ -67,11 +76,19 @@ warm_package() {
 }
 
 check_claude_config() {
-  python3 - <<'PY'
+  CLAUDE_CONFIG_DIR="$CLAUDE_CONFIG_DIR" python3 - <<'PY'
 import json
+import os
 from pathlib import Path
-p = Path.home() / ".claude" / "settings.json"
-if not p.exists():
+# Claude reads MCP definitions from .claude.json, not settings.json. The
+# settings.json fallback preserves legacy operator flows until their config is migrated.
+config_dir = os.environ.get("CLAUDE_CONFIG_DIR")
+p = Path(config_dir) / ".claude.json" if config_dir else Path.home() / ".claude.json"
+if not p.exists() and not config_dir:
+    p = Path.home() / ".claude" / "settings.json"
+# Only explicit fleet seats require a private, non-symlink config. Operator
+# config remains compatible with pre-existing permission conventions.
+if not p.exists() or p.is_symlink() or (config_dir and (p.stat().st_mode & 0o077) != 0):
     raise SystemExit(1)
 try:
     data = json.loads(p.read_text(encoding="utf-8"))
@@ -92,10 +109,15 @@ PY
 }
 
 apply_claude_config() {
-  python3 - <<'PY'
+  CLAUDE_CONFIG_DIR="$CLAUDE_CONFIG_DIR" python3 - <<'PY'
 import json
+import os
 from pathlib import Path
-p = Path.home() / ".claude" / "settings.json"
+# Claude reads MCP definitions from .claude.json for both operator and
+# explicitly isolated fleet config dirs. The checker retains a settings.json
+# fallback only to avoid breaking legacy operator configurations.
+config_dir = os.environ.get("CLAUDE_CONFIG_DIR")
+p = Path(config_dir) / ".claude.json" if config_dir else Path.home() / ".claude.json"
 p.parent.mkdir(parents=True, exist_ok=True)
 if p.exists():
     try:
@@ -117,7 +139,7 @@ PY
 }
 
 check_codex_config() {
-  local cfg="$HOME/.codex/config.toml"
+  local cfg="${CODEX_HOME:-$HOME/.codex}/config.toml"
   [[ -f "$cfg" ]] || return 1
   grep -Eq '^\[mcp_servers\.(sequential-thinking|sequential_thinking)\]' "$cfg" && \
   grep -q '^command = "npx"' "$cfg" && \
@@ -125,7 +147,7 @@ check_codex_config() {
 }
 
 apply_codex_config() {
-  local cfg="$HOME/.codex/config.toml"
+  local cfg="${CODEX_HOME:-$HOME/.codex}/config.toml"
   mkdir -p "$(dirname "$cfg")"
   [[ -f "$cfg" ]] || touch "$cfg"
 
@@ -148,10 +170,11 @@ apply_codex_config() {
 }
 
 check_opencode_config() {
-  python3 - <<'PY'
+  XDG_CONFIG_HOME="${XDG_CONFIG_HOME:-}" python3 - <<'PY'
 import json
+import os
 from pathlib import Path
-p = Path.home() / ".config" / "opencode" / "config.json"
+p = Path(os.environ["XDG_CONFIG_HOME"]) / "opencode" / "config.json" if os.environ.get("XDG_CONFIG_HOME") else Path.home() / ".config" / "opencode" / "config.json"
 if not p.exists():
     raise SystemExit(1)
 try:
@@ -174,10 +197,11 @@ PY
 }
 
 apply_opencode_config() {
-  python3 - <<'PY'
+  XDG_CONFIG_HOME="${XDG_CONFIG_HOME:-}" python3 - <<'PY'
 import json
+import os
 from pathlib import Path
-p = Path.home() / ".config" / "opencode" / "config.json"
+p = Path(os.environ["XDG_CONFIG_HOME"]) / "opencode" / "config.json" if os.environ.get("XDG_CONFIG_HOME") else Path.home() / ".config" / "opencode" / "config.json"
 p.parent.mkdir(parents=True, exist_ok=True)
 if p.exists():
     try: