Replaces the per-directory shadow-repo design with a single shared shadow
git store at ~/.hermes/checkpoints/store/. Object DB is now deduplicated
across every working directory the agent has ever touched; a dozen
worktrees of the same project cost near-zero in additional disk.
Why
---
Pre-v2 design had three compounding problems that let ~/.hermes/checkpoints/
grow to multi-GB on active machines:
1. Each working directory got its own full shadow git repo — no object
dedup across projects or across worktrees of the same project.
2. _prune() was a documented no-op: max_snapshots only limited the
/rollback listing. Loose objects accumulated forever.
3. Defaults: enabled=True, auto_prune=False — users paid the disk cost
without ever asking for /rollback.
Field report on a single workstation: 847 MB across 47 shadow repos,
mostly redundant clones of the hermes-agent source tree.
Changes
-------
- tools/checkpoint_manager.py: full rewrite. Single bare store, per-project
refs (refs/hermes/<hash>), per-project indexes (store/indexes/<hash>),
per-project metadata (store/projects/<hash>.json with workdir +
created_at + last_touch). On first v2 init, any pre-v2 per-directory
shadow repos are auto-migrated into legacy-<timestamp>/ so the new
store starts clean. _prune() now actually rewrites the per-project ref
to the last max_snapshots commits and runs git gc --prune=now. New
_enforce_size_cap() drops oldest commits round-robin across projects
when the store exceeds max_total_size_mb. _drop_oversize_from_index()
filters any single file larger than max_file_size_mb out of the snapshot.
- hermes_cli/checkpoints.py: new 'hermes checkpoints' CLI
(status / list / prune / clear / clear-legacy) for managing the store
outside a session.
- hermes_cli/config.py: flipped defaults — enabled=False, max_snapshots=20,
auto_prune=True. Added max_total_size_mb=500, max_file_size_mb=10.
Tightened DEFAULT_EXCLUDES (added target/, *.so/*.dylib/*.dll,
*.mp4/*.mov, *.zip/*.tar.gz, .worktrees/, .mypy_cache/, etc.).
- run_agent.py / cli.py / gateway/run.py: thread the new kwargs through
AIAgent and the startup auto_prune hooks.
- Tests rewritten to match v2 storage while keeping backwards-compat
coverage for the pre-v2 prune path (per-directory shadow repos under
base/ are still swept correctly for anyone mid-migration).
- Docs updated: user-guide/checkpoints-and-rollback.md explains the
shared store, new defaults, migration, and the new CLI;
reference/cli-commands.md documents 'hermes checkpoints'.
E2E validated
-------------
- Legacy migration: pre-v2 shadow repos auto-archived into legacy-<ts>/.
- Object dedup: two projects with an identical shared.py blob resolve to
7 total objects in the store (v1 would have stored the blob twice).
- max_snapshots=3 actually enforced: after 6 commits, list shows 3.
- Orphan prune: deleting a project's workdir + 'hermes checkpoints prune
--retention-days 0' removes its ref, index, and metadata; GC reclaims
the objects.
- max_file_size_mb=1 excludes a 2 MB weights.bin while keeping the
tracked source code files.
- hermes checkpoints {status,prune,clear,clear-legacy} all work from the
CLI without an agent running.
Breaking / migration
--------------------
No in-place data migration — legacy per-directory shadow repos are moved
into legacy-<timestamp>/ on first run. Old /rollback history is still
accessible by inspecting the archive with git; run
'hermes checkpoints clear-legacy' to reclaim the space when ready. Users
relying on /rollback must now set checkpoints.enabled=true (or pass
--checkpoints) explicitly.
Every working dir hermes ever touches gets its own shadow git repo under
~/.hermes/checkpoints/{sha256(abs_dir)[:16]}/. The per-repo _prune is a
no-op (comment in CheckpointManager._prune says so), so abandoned repos
from deleted/moved projects or one-off tmp dirs pile up forever. Field
reports put the typical offender at 1000+ repos / ~12 GB on active
contributor machines.
Adds an opt-in startup sweep that mirrors the sessions.auto_prune
pattern from #13861 / #16286:
- tools/checkpoint_manager.py: new prune_checkpoints() and
maybe_auto_prune_checkpoints() helpers. Deletes shadow repos that
are orphan (HERMES_WORKDIR marker points to a path that no longer
exists) or stale (newest in-repo mtime older than retention_days).
Idempotent via a CHECKPOINT_BASE/.last_prune marker file so it only
runs once per min_interval_hours regardless of how many hermes
processes start up.
- hermes_cli/config.py: new checkpoints.auto_prune /
retention_days / delete_orphans / min_interval_hours knobs.
Default auto_prune: false so users who rely on /rollback against
long-ago sessions never lose data silently.
- cli.py / gateway/run.py: startup hooks gated on checkpoints.auto_prune,
called right next to the existing state.db maintenance block.
- Docs updated with the new config knobs.
- 11 regression tests: orphan/stale deletion, precedence, byte-freed
tracking, non-shadow dir skip, interval gating, corrupt marker
recovery.
Refs #3015 (session-file disk growth was fixed in #16286; this covers
the checkpoint side noted out-of-scope there).
Make the main-branch test suite pass again. Most failures were tests
still asserting old shapes after recent refactors; two were real source
bugs.
Source fixes:
- tools/mcp_tool.py: _kill_orphaned_mcp_children() slept 2s on every
shutdown even when no tracked PIDs existed, making test_shutdown_is_parallel
measure ~3s for 3 parallel 1s shutdowns. Early-return when pids is empty.
- hermes_cli/tips.py: tip 105 was 157 chars; corpus max is 150.
Test fixes (mostly stale mock targets / missing fixture fields):
- test_zombie_process_cleanup, test_agent_cache: patch run_agent.cleanup_vm
(the local name bound at import), not tools.terminal_tool.cleanup_vm.
- test_browser_camofox: patch tools.browser_camofox.load_config, not
hermes_cli.config.load_config (the source module, not the resolved one).
- test_flush_memories_codex._chat_response_with_memory_call: add
finish_reason, tool_call.id, tool_call.type so the chat_completions
transport normalizer doesn't AttributeError.
- test_concurrent_interrupt: polling_tool signature now accepts
messages= kwarg that _invoke_tool() passes through.
- test_minimax_provider: add _fallback_chain=[] to the __new__'d agent
so switch_model() doesn't AttributeError.
- test_skills_config: SKILLS_DIR MagicMock + .rglob stopped working
after the scanner switched to agent.skill_utils.iter_skill_index_files
(os.walk-based). Point SKILLS_DIR at a real tmp_path and patch
agent.skill_utils.get_external_skills_dirs.
- test_browser_cdp_tool: browser_cdp toolset was intentionally split into
'browser-cdp' (commit 96b0f3700) so its stricter check_fn doesn't gate
the whole browser toolset; test now expects 'browser-cdp'.
- test_registry: add tools.browser_dialog_tool to the expected
builtin-discovery set (PR #14540 added it).
- test_file_tools TestPatchHints: patch_tool surfaces hints as a '_hint'
key on the JSON payload, not inline '[Hint: ...' text.
- test_write_deny test_hermes_env: resolve .env via get_hermes_home() so
the path matches the profile-aware denylist under hermetic HERMES_HOME.
- test_checkpoint_manager test_falls_back_to_parent: guard the walk-up
so a stray /tmp/pyproject.toml on the host doesn't pick up /tmp as the
project root.
- test_quick_commands: set cli.session_id in the __new__'d CLI so the
alias-args path doesn't trip AttributeError when fuzzy-matching leaks
a skill command across xdist test distribution.
Users with 'commit.gpgsign = true' in their global git config got a
pinentry popup (or a failed commit) every time the agent took a
background filesystem snapshot — every write_file, patch, or diff
mid-session. With GPG_TTY unset, pinentry-qt/gtk would spawn a GUI
window, constantly interrupting the session.
The shadow repo is internal Hermes infrastructure. It must not
inherit user-level git settings (signing, hooks, aliases, credential
helpers, etc.) under any circumstance.
Fix is layered:
1. _git_env() sets GIT_CONFIG_GLOBAL=os.devnull,
GIT_CONFIG_SYSTEM=os.devnull, and GIT_CONFIG_NOSYSTEM=1. Shadow
git commands no longer see ~/.gitconfig or /etc/gitconfig at all
(uses os.devnull for Windows compat).
2. _init_shadow_repo() explicitly writes commit.gpgsign=false and
tag.gpgSign=false into the shadow's own config, so the repo is
correct even if inspected or run against directly without the
env vars, and for older git versions (<2.32) that predate
GIT_CONFIG_GLOBAL.
3. _take() passes --no-gpg-sign inline on the commit call. This
covers existing shadow repos created before this fix — they will
never re-run _init_shadow_repo (it is gated on HEAD not existing),
so they would miss layer 2. Layer 1 still protects them, but the
inline flag guarantees correctness at the commit call itself.
Existing checkpoints, rollback, list, diff, and restore all continue
to work — history is untouched. Users who had the bug stop getting
pinentry popups; users who didn't see no observable change.
Tests: 5 new regression tests in TestGpgAndGlobalConfigIsolation,
including a full E2E repro with fake HOME, global gpgsign=true, and
a deliberately broken GPG binary — checkpoint succeeds regardless.
Adds _normalize_path() helper that calls expanduser().resolve() to
properly handle tilde paths (e.g. ~/.hermes, ~/.config). Previously
Path.resolve() alone treated ~ as a literal directory name, producing
invalid paths like /root/~/.hermes.
Also improves _run_git() error handling to distinguish missing working
directories from missing git executable, and adds pre-flight directory
validation.
Cherry-picked from PR #7898 by faishal882.
Fixes#7807
This commit addresses a security vulnerability where unsanitized user inputs for commit_hash and file_path were passed directly to git commands in CheckpointManager.restore() and diff(). It validates commit hashes to be strictly hexadecimal characters without leading dashes (preventing flag injection like '--patch') and enforces file paths to stay within the working directory via root resolution. Regression tests test_restore_rejects_argument_injection, test_restore_rejects_invalid_hex_chars, and test_restore_rejects_path_traversal were added.
- treat git diff --cached --quiet rc=1 as an expected checkpoint state
instead of logging it as an error
- downgrade expected write PermissionError/EROFS/EACCES failures out of
error logging while keeping unexpected exceptions at error level
- add regression tests for both logging behaviors
Automatic filesystem snapshots before destructive file operations,
with user-facing rollback. Inspired by PR #559 (by @alireza78a).
Architecture:
- Shadow git repos at ~/.hermes/checkpoints/{hash}/ via GIT_DIR
- CheckpointManager: take/list/restore, turn-scoped dedup, pruning
- Transparent — the LLM never sees it, no tool schema, no tokens
- Once per turn — only first write_file/patch triggers a snapshot
Integration:
- Config: checkpoints.enabled + checkpoints.max_snapshots
- CLI flag: hermes --checkpoints
- Trigger: run_agent.py _execute_tool_calls() before write_file/patch
- /rollback slash command in CLI + gateway (list, restore by number)
- Pre-rollback snapshot auto-created on restore (undo the undo)
Safety:
- Never blocks file operations — all errors silently logged
- Skips root dir, home dir, dirs >50K files
- Disables gracefully when git not installed
- Shadow repo completely isolated from project git
Tests: 35 new tests, all passing (2798 total suite)
Docs: feature page, config reference, CLI commands reference
