fix(security): tighten .env file permissions to 0600 at all creation sites

.env holds API keys and secrets. Multiple creation sites used `cp` /
`touch` / `shutil.copy2` which obey the process umask — commonly
0o022, leaving the file at 0o644 (world-readable). Apply chmod 0o600
explicitly at every site that creates or copies .env.

Sites covered:
- docker/stage2-hook.sh: after the seed_one '.env' call, applied
  unconditionally (not just on first-seed) so a host-mounted .env with
  loose perms gets tightened on every container restart
- hermes_cli/doctor.py: 'hermes doctor --fix' touches an empty .env
  when missing
- hermes_cli/profiles.py: 'hermes profile create --clone' copies .env
  from the source profile; shutil.copy2 preserves source mode, so a
  source .env at 0o644 was being cloned into 0o644
- setup-hermes.sh: in-tree setup script's cp .env.example .env path,
  plus the already-exists branch (mirror of install.sh which already
  chmods 600 unconditionally on line 1442)

scripts/install.sh was NOT changed — it already chmod 600's the .env
unconditionally after the create/already-exists branches (line 1442).

Salvaged from PR #25726 by @dusterbloom. The docker/entrypoint.sh
portion of the original PR was dropped because main switched to an
s6-overlay shim — the .env creation logic moved to stage2-hook.sh,
which is where the chmod now lives.

Closes #25497 (subset — install.sh + setup-hermes.sh) and #8448
(subset — install.sh only) as superseded.

Co-authored-by: teknium1 <127238744+teknium1@users.noreply.github.com>

hermes_cli/doctor.py

@@ -569,6 +569,13 @@ def run_doctor(args):
             if should_fix:
                 env_path.parent.mkdir(parents=True, exist_ok=True)
                 env_path.touch()
+                # .env holds API keys — restrict to owner-only access from
+                # creation. touch() obeys umask which is commonly 0o022,
+                # leaving the file world-readable; tighten explicitly.
+                try:
+                    os.chmod(str(env_path), 0o600)
+                except OSError:
+                    pass
                 check_ok(f"Created empty {_DHH}/.env")
                 check_info("Run 'hermes setup' to configure API keys")
                 fixed_count += 1

hermes_cli/profiles.py

@@ -723,7 +723,17 @@ def create_profile(
             for filename in _CLONE_CONFIG_FILES:
                 src = source_dir / filename
                 if src.exists():
-                    shutil.copy2(src, profile_dir / filename)
+                    dst = profile_dir / filename
+                    shutil.copy2(src, dst)
+                    # Tighten .env to owner-only after copy. shutil.copy2
+                    # preserves source mode bits, but if the source's .env
+                    # was loose (host umask 0o022 leaving 0o644), tighten
+                    # explicitly so the clone doesn't inherit weak perms.
+                    if filename == ".env":
+                        try:
+                            os.chmod(str(dst), 0o600)
+                        except OSError:
+                            pass
 
             # Clone installed skills from the source profile. The dashboard's
             # "clone from default" flow is expected to preserve both bundled