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fix: hash-check before deletion, track all files, fix overrides bug, update help text

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- remove_tracked_files: always compare SHA-256 hash before deleting,
  even when called with explicit files dict; skip modified files unless
  --force is set (was unconditionally deleting all tracked files)
- finalize_setup: track ALL files from setup() (no agent-root filter);
  safe because removal now checks hashes
- list_all_agents: track embedded versions in separate dict so overrides
  always reference the correct embedded version, not a catalog/project
  pack that overwrote the seen dict
- --ai-skills help text: updated to say 'requires --ai or --agent'
This commit is contained in:
Manfred Riem
2026-03-23 11:24:53 -05:00
parent 34fa61e1cc
commit 48392ea865
2 changed files with 20 additions and 14 deletions
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2
src/specify_cli/__init__.py
View File

@@ -1725,7 +1725,7 @@ def init(
skip_tls: bool = typer.Option(False, "--skip-tls", help="Skip SSL/TLS verification (not recommended)"),
debug: bool = typer.Option(False, "--debug", help="Show verbose diagnostic output for network and extraction failures"),
github_token: str = typer.Option(None, "--github-token", help="GitHub token to use for API requests (or set GH_TOKEN or GITHUB_TOKEN environment variable)"),
ai_skills: bool = typer.Option(False, "--ai-skills", help="Install Prompt.MD templates as agent skills (requires --ai)"),
ai_skills: bool = typer.Option(False, "--ai-skills", help="Install Prompt.MD templates as agent skills (requires --ai or --agent)"),
offline: bool = typer.Option(False, "--offline", help="Use assets bundled in the specify-cli package instead of downloading from GitHub (no network access required). Bundled assets will become the default in v0.6.0 and this flag will be removed."),
preset: str = typer.Option(None, "--preset", help="Install a preset during initialization (by preset ID)"),
branch_numbering: str = typer.Option(None, "--branch-numbering", help="Branch numbering strategy: 'sequential' (001, 002, ...) or 'timestamp' (YYYYMMDD-HHMMSS)"),

32
src/specify_cli/agent_pack.py
View File

@@ -346,21 +346,17 @@ class AgentBootstrap:
the agent's directory tree for anything additional.
All files returned by ``setup()`` are tracked — including shared
project infrastructure — so that teardown/switch can precisely
remove everything the agent installed. This is intentional:
``remove_tracked_files()`` only deletes files whose SHA-256
hash still matches the original, so user-modified files are
always preserved (unless ``--force`` is used).
project infrastructure — so that teardown/switch can detect
modifications. ``remove_tracked_files()`` compares SHA-256
hashes before deleting and will only remove files whose hash
still matches, preserving any user-modified files (unless
``--force`` is used).
Args:
agent_files: Files reported by :meth:`setup`.
extension_files: Files created by extension registration.
"""
all_extension = list(extension_files or [])
# Track ALL files returned by setup(), not just those under the
# agent's directory tree. This is safe because teardown only
# removes files that are unmodified (hash check) and prompts
# for confirmation on modified files.
all_agent: List[Path] = list(agent_files or [])
# Scan the agent's directory tree for files created by later
@@ -641,9 +637,13 @@ def remove_tracked_files(
)
removed: List[str] = []
for rel_path in entries:
for rel_path, original_hash in entries.items():
abs_path = project_path / rel_path
if abs_path.is_file():
if original_hash and _sha256(abs_path) != original_hash:
# File was modified since installation — skip unless forced
if not force:
continue
abs_path.unlink()
removed.append(rel_path)
@@ -792,6 +792,11 @@ def list_all_agents(project_path: Optional[Path] = None) -> List[ResolvedPack]:
"""
seen: dict[str, ResolvedPack] = {}
# Track embedded versions separately so overrides can accurately
# reference what they replace, even after catalog/project/user
# packs have overwritten the seen dict entry.
embedded_versions: dict[str, str] = {}
# Start from lowest priority (embedded) so higher priorities overwrite
for manifest in list_embedded_agents():
seen[manifest.id] = ResolvedPack(
@@ -799,6 +804,7 @@ def list_all_agents(project_path: Optional[Path] = None) -> List[ResolvedPack]:
source="embedded",
path=manifest.pack_path or _embedded_agents_dir() / manifest.id,
)
embedded_versions[manifest.id] = manifest.version
# Catalog cache
catalog_dir = _catalog_agents_dir()
@@ -808,7 +814,7 @@ def list_all_agents(project_path: Optional[Path] = None) -> List[ResolvedPack]:
if child.is_dir() and mf.is_file():
try:
m = AgentManifest.from_yaml(mf)
overrides = f"embedded v{seen[m.id].manifest.version}" if m.id in seen else None
overrides = f"embedded v{embedded_versions[m.id]}" if m.id in embedded_versions else None
seen[m.id] = ResolvedPack(manifest=m, source="catalog", path=child, overrides=overrides)
except AgentPackError:
continue
@@ -822,7 +828,7 @@ def list_all_agents(project_path: Optional[Path] = None) -> List[ResolvedPack]:
if child.is_dir() and mf.is_file():
try:
m = AgentManifest.from_yaml(mf)
overrides = f"embedded v{seen[m.id].manifest.version}" if m.id in seen else None
overrides = f"embedded v{embedded_versions[m.id]}" if m.id in embedded_versions else None
seen[m.id] = ResolvedPack(manifest=m, source="project", path=child, overrides=overrides)
except AgentPackError:
continue
@@ -835,7 +841,7 @@ def list_all_agents(project_path: Optional[Path] = None) -> List[ResolvedPack]:
if child.is_dir() and mf.is_file():
try:
m = AgentManifest.from_yaml(mf)
overrides = f"embedded v{seen[m.id].manifest.version}" if m.id in seen else None
overrides = f"embedded v{embedded_versions[m.id]}" if m.id in embedded_versions else None
seen[m.id] = ResolvedPack(manifest=m, source="user", path=child, overrides=overrides)
except AgentPackError:
continue