fix(update): also ignore the flat-install config/credential/profile roots

The same `git stash push --include-untracked` sweep that took state.db
on a flat install (#110648) also takes every other untracked file at the
$HERMES_HOME root: config.yaml, auth.json/auth.lock, memories/,
profiles/, .credentials/, mcp-tokens/ and pairing/. Losing those on a
declined or failed restore strands the user's credentials and profile
config just as badly as losing the session store.

Extend the root-anchored block with those paths (none are tracked or
already ignored on main) and append them to the test's
FLAT_INSTALL_RUNTIME_STATE list so the existing stash invariant covers
them without a new test.

.gitignore

@@ -172,8 +172,9 @@ docs/superpowers/*
 # with HERMES_INSTALL_DIR=$HERMES_HOME or by older installers): the live session
 # store, its SQLite sidecars and retired-WAL capture dirs, quick snapshots, the
 # legacy transcripts, the cron job store (jobs.json) and executions ledger,
-# gateway lock/pid files, and cache/spill directories are Hermes-managed runtime
+# gateway lock/pid files, cache/spill directories, and the profile's own
-# state, never code changes.
+# config/credential/memory/profile roots are Hermes-managed runtime state,
+# never code changes.
 # Ignore them so `hermes update`'s `git stash push --include-untracked` cannot
 # sweep the live state.db/-wal into the stash and unlink it under the running
 # gateway (#110648). Nested installs keep all of this under $HERMES_HOME outside
@@ -196,6 +197,14 @@ docs/superpowers/*
 /gateway.pid
 /hook_outputs/
 /cache/
+/config.yaml
+/auth.json
+/auth.lock
+/memories/
+/profiles/
+/.credentials/
+/mcp-tokens/
+/pairing/
 
 # Persistent dev sandbox dir (scripts/dev-sandbox.sh --persistent)
 .hermes-sandbox/

tests/hermes_cli/test_update_flat_install_state_gitignore.py

@@ -22,7 +22,8 @@ REPO_ROOT = Path(__file__).resolve().parents[2]
 # (gateway/platforms/base.py _ROOT_CREDENTIAL_PATHS enumerates the same set) and
 # retired-WAL capture dirs, quick snapshots, the legacy transcript dir, the
 # default kanban board, the cron job store (cron/jobs.py JOBS_FILE) and
-# executions ledger, gateway lock/pid files and the cache/spill directories.
+# executions ledger, gateway lock/pid files, the cache/spill directories and the
+# config/auth/memory/profile/credential/pairing roots.
 FLAT_INSTALL_RUNTIME_STATE = (
     "state.db",
     "state.db-wal",
@@ -42,6 +43,14 @@ FLAT_INSTALL_RUNTIME_STATE = (
     "gateway.pid",
     "hook_outputs/2026-09-14_06-00-00/tool.json",
     "cache/banner_snapshot.json",
+    "config.yaml",
+    "auth.json",
+    "auth.lock",
+    "memories/MEMORY.md",
+    "profiles/work/config.yaml",
+    ".credentials/github_token",
+    "mcp-tokens/server.json",
+    "pairing/telegram.json",
 )