Commit Graph

25 Commits

Author SHA1 Message Date
Noor ul ain
cf71d00dfe fix(workflows): reject a retry gate whose verdict enum forbids the reset value (#3912)
A gate with `on_reject: retry` consumes a bound reject verdict before
pausing by resetting the named input to `""` (documented behaviour, so a
later resume prompts again). Every `resume()` re-resolves the persisted
inputs through `_coerce_input`.

Those two rules collide when the bound input declares an `enum` that does
not list `""`. The reset writes a value the input's own enum forbids, and
the run wedges:

    inputs:
      spec_verdict:
        type: string
        enum: [approve, reject]
    steps:
      - id: review
        type: gate
        options: [approve, reject]
        on_reject: retry
        verdict_input: spec_verdict

    $ specify workflow run wf --input spec_verdict=reject
    Status: paused
    $ specify workflow resume <run_id> --input note=b
    Error: Input 'spec_verdict' value '' not in allowed values:
           ['approve', 'reject'].

The workflow validates clean and the first run looks fine, so the failure
only appears at the second resume. It is also unrecoverable in practice:
`_resolve_inputs` re-coerces the whole persisted map, so *any* resume that
supplies an input dies on the stored `""`. Only a resume with no inputs at
all still works -- and that is precisely the call that cannot deliver a new
verdict, which is the one thing the retry cycle exists to allow.

Extend the existing `verdict_input` cross-check (which already confirms the
name is declared) to also require that a retry-bound input's `enum` admits
the reset sentinel, and report it with a fix hint. To do that, thread the
input *definitions* through `_validate_steps` instead of just their names.

Rejected the alternative of popping the key instead of writing `""`: that
lets the input's `default` flow back in on the next resume, so a gate the
user just rejected would silently auto-approve.

Docs: note the `enum` requirement next to the reset behaviour it follows
from.

Adds 4 validation tests for the new guard plus a characterization test that
drives the engine directly to pin the wedge it prevents.

Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>

Assisted-by: Claude Opus 5 (1M context)
2026-07-31 09:53:25 -05:00
Markus Wondrak
675143591d feat: bind gate verdict to workflow input via verdict_input (#3725)
* feat: bind gate verdict to workflow input via verdict_input

Add an optional `verdict_input` field to gate steps that lets an
external system supply a verdict through a declared workflow input
instead of an interactive TTY prompt.

When the referenced input carries a non-empty string value that
matches one of the gate's `options` (case-insensitive), the gate
auto-decides, records the matched spelling in `output.choice`, and
applies the existing `on_reject` / abort / skip / retry semantics.
If the value is present but does not match an option, or is a
non-string, the gate fails immediately with a clear error message.
When the input is absent, null, or empty, the gate falls back to
today's TTY-prompt-or-pause behaviour unchanged.

The engine now persists `result.error` alongside each step's status
and output so that failed-step error messages survive across runs.
The CLI (`workflow run` and `workflow resume`) surfaces these
persisted errors after a failed or aborted run. `validate_workflow`
cross-references `verdict_input` against the workflow's declared
inputs block and reports an error for undeclared names, consistent
with the existing `wait_for` id cross-check.

Closes discussion: https://github.com/github/spec-kit/discussions/3717

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>
Assisted-by: GitHub Copilot (model: claude-sonnet-4.6, autonomous)

* Potential fix for pull request finding

Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com>

* Fix workflow JSON error payloads

Include persisted step errors in _workflow_run_payload so workflow run/resume/status --json all surface failure reasons consistently. Add JSON-path tests for failed and successful runs.

Assisted-by: GitHub Copilot (model: gpt-5.3-codex, autonomous)

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

* Potential fix for pull request finding

Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com>

* fix(workflows): reject verdict inputs in fan-out

Fan-out items share workflow inputs and cannot safely consume a bound gate verdict. Reject verdict_input bindings during validation and at runtime while preserving unbound gates.

Assisted-by: GitHub Copilot (model: GPT-5.6 Sol, autonomous)

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

* fix: update workflow command handling

Assisted-by: GitHub Copilot (model: gpt-5.3-codex, autonomous)

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

---------

Co-authored-by: Markus <markus@example.com>
Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>
Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com>
2026-07-30 07:39:49 -05:00
Ali jawwad
103ad73775 fix(workflows): guard non-mapping 'workflow:' block in WorkflowDefinition (#3694)
* fix(workflows): guard non-mapping 'workflow:' block in WorkflowDefinition

A present-but-non-mapping top-level `workflow:` block (bare `workflow:` ->
YAML null, or `workflow: <str>` / `workflow: [..]`) crashed
WorkflowDefinition.__init__ with AttributeError: the `{}` default of
`data.get("workflow", {})` only applies when the key is ABSENT, so a non-dict
value reached `workflow.get("id", ...)`. This fires inside from_yaml/
from_string — before validate_workflow can report the malformed shape — and
in the CLI escapes as a raw traceback (load_workflow is wrapped to catch only
FileNotFoundError/ValueError).

Normalize the local `workflow` to {} when it is not a mapping (self.data keeps
the raw value so validate_workflow still reports it), mirroring the adjacent
default_options guard.

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

* test(workflows): assert self.data preserves the raw non-mapping workflow value

Address review: the previous assertion only proved the key stayed present; it
would pass even if construction replaced the malformed value with {}. Assert
definition.data["workflow"] equals the original parsed value and is still a
non-mapping, proving the guard normalizes only the local variable.

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

---------

Co-authored-by: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
2026-07-27 09:10:51 -05:00
Ali jawwad
ea6843c1fe fix(workflows): guard non-mapping 'inputs:' block in engine._resolve_inputs (#3696)
execute()/resume() run UNVALIDATED definitions (load_workflow does not
validate). WorkflowDefinition stores `inputs` raw, so a non-mapping
`inputs:` block (bare `inputs:` -> None, or `inputs: []`) crashed
_resolve_inputs at `for name, input_def in definition.inputs.items()` with
AttributeError, aborting the whole run.

Return {} when inputs is not a mapping, mirroring validate_workflow's own
`isinstance(definition.inputs, dict)` check. Protects both call sites
(execute and resume); normal dict resolution is unchanged.

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-authored-by: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
2026-07-24 10:52:28 -05:00
Noor ul ain
d7699c39f2 fix(workflows): reject non-list input 'enum' instead of crashing (#3601)
A workflow input whose `enum` is a scalar or string (e.g. `enum: 5`,
`enum: "abc"`) previously slipped past `validate_workflow` and crashed
at run time. The `value not in enum_values` membership test in
`_coerce_input` raises a raw `TypeError` ("argument of type 'int' is
not iterable") for a scalar, and a bare string turns enum membership
into a silent substring test. The `TypeError` also escapes
`validate_workflow`'s `except ValueError`, breaking its documented
"return a list of errors, never raise" contract.

This is the same unvalidated-`execute()` crash class as the fan-in
`wait_for` (#3482) and fan-out step-template (#3537) fixes: `validate()`
should reject the value, but the value can still reach the engine via
`execute()`, which accepts unvalidated definitions.

Fix:
- `_coerce_input` requires a list `enum` (or `None`), raising a clean
  ValueError for any other shape — so both `validate_workflow` and
  runtime `_resolve_inputs` fail fast with a clear message.
- `validate_workflow` checks `enum` shape directly (not only via the
  default-coercion path, which is reached only when a `default` exists),
  and strips a malformed `enum` before coercing the default so the
  wrong-typed-default error is not duplicated as an enum-shape error.
- The `integration: auto` sentinel only strips a *list* `enum`; a
  non-list `enum` stays in the definition so it is rejected rather than
  silently exempted by the `auto` membership skip.

Tests cover all three layers: `_coerce_input` directly, authoring-time
`validate_workflow` (with no default present), and runtime
`_resolve_inputs`, plus the `integration: auto` interaction.

Co-authored-by: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
2026-07-21 13:09:38 -05:00
Markus Wondrak
d6fa0460ed feat(workflows): WorkflowResolver standalone (PR 1) (#3557)
* feat(workflows): add standalone WorkflowResolver and overlay subsystem

Implement PR 1 of the workflow-overlays plan: a concrete, standalone
WorkflowResolver for downstream workflow extensibility without touching the
Preset subsystem.

- Add overlay manifest schema (Overlay, OverlayEdit, validate_overlay_yaml)
- Add pure-function merge engine (find_step, apply_edit, merge_steps,
  validate_edits) with recursive anchor search and higher-wins semantics
- Add StepListComposer and tiered layer sources (project, installed, base)
- Add WorkflowResolver facade with inline HIGHER_WINS priority sorting
- Add CLI verbs: workflow overlay add/set-priority/enable/disable/remove/list
  and workflow resolve <id>
- Wire WorkflowEngine.load_workflow through WorkflowResolver
- Extend workflow add to copy optional overlays/ subdirectory from local
  workflow directories
- Add comprehensive unit, integration, and security tests

Refs: discussion #3473 (https://github.com/github/spec-kit/discussions/3473)

Assisted-by: Kimi (model: opencode-go/kimi-k2.7-code, autonomous)

* fix(workflows): reject symlinked overlay directories in layer sources

Address PR #3557 review comments r3594064534 and r3594064563:

- ProjectOverlaySource.collect now rejects symlinked per-workflow overlay
  directories (.specify/workflows/overlays/<id>) before iterating
- InstalledOverlaySource.collect now rejects symlinked installed overlay
  directories (.specify/workflows/<id>/overlays) before iterating
- workflow_overlay_list catches ValueError from resolver and exits with
  code 1 instead of crashing on unhandled exceptions
- Added .specify/workflows/overlays to _reject_unsafe_workflow_storage
  chokepoint for defense-in-depth

These guards prevent symlinked overlay directories from redirecting
auto-loaded overlay YAML to attacker-controlled content outside the
project, which could inject executable shell steps into trusted workflows.

Refs: PR #3557 review comments r3594064534, r3594064563

Assisted-by: opencode-go/qwen3.7-max (autonomous)

* fix(workflows): address Copilot review findings in merge engine

- Apply inserts before winning replace to prevent anchor-not-found errors
  when replace changes step ID (r3594064604)
- Track attribution recursively for nested steps in composite inserts/replaces
  so workflow resolve attributes all child steps correctly (r3594064638)
- Add regression tests for both fixes

Refs: PR #3557 review discussion

Assisted-by: GitHub Copilot (model: qwen3.7-plus, autonomous)

* refactor(workflows): simplify overlay architecture to 2-tier

Remove installed overlays tier to enforce clean separation of concerns:
- workflow add installs workflows only (no overlay copying)
- workflow overlay add installs overlays only (project-local)

Changes:
- Remove InstalledOverlaySource class and all references
- Remove overlay-copying logic from _validate_and_install_local()
- Update WorkflowResolver to 2-tier: project overlays + base workflow
- Fix --priority override timing: apply before validation, not after
- Remove tests for installed overlays (no longer applicable)

Rationale: If upstream controls both base workflow and shipped overlays,
and both get overwritten on bundle update, there's no reason to ship
overlays separately. Overlays only make sense when someone other than
the base author adds them.

Resolves all three review findings from PR #3557:
- r3594064677: workflow add no longer copies overlays from all call sites
- r3594064705: --priority override now applied before validation
- r3594064726: no stale installed overlays (tier removed entirely)

Assisted-by: Claude (model: claude-opus-4-7, autonomous)

* fix(workflows): harden overlay symlink handling

Assisted-by: GitHub Copilot (model: GPT-5.4, autonomous)

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

* docs(workflows): remove stale installed-overlay references from workflows.md

The 2-tier refactor (cc28185) removed the installed-overlay tier entirely,
but docs/reference/workflows.md was not updated. This commit addresses all
four Cluster 2 findings from the PR review:

- workflow add: remove sentence about copying overlays/ subdirectory
- How Overlays Work: drop installed-overlay table row and precedence prose;
  rewrite to 2-tier model (project overlays only, source-order tie-break)
- overlay remove: drop trailing sentence about installed overlays
- Interaction with Bundles: rewrite to say workflow add installs only
  workflow.yml; remove installed-overlay discovery language

Fixes: r3596368791, r3596368831, r3596368873, r3596368919

Assisted-by: GitHub Copilot (model: claude-sonnet-4.6, autonomous)
Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

* fix(overlays): detect ancestor-conflict anchors in merge_steps

When two overlay edits target anchors that share a parent/descendant
relationship (e.g. remove an if-step + insert_after a nested child),
merge_steps processed them independently and in dict-insertion order,
making the outcome non-deterministic.

Add two private helpers to merge.py:
- _descendant_ids(step): returns all step IDs nested inside a step dict
  by delegating to the existing _all_base_step_ids helper on children.
- _check_anchor_conflicts(anchors, base_steps): for each targeted anchor
  finds its descendants and checks whether any other targeted anchor is
  among them; returns human-readable error strings.

Wire _check_anchor_conflicts into merge_steps immediately after
edits_by_anchor is built, before any tree mutation occurs. Raises
ValueError listing the conflicting anchor pair(s) so overlay authors
know exactly what to fix.

Add TestMergeStepsAncestorConflicts (6 cases):
- remove parent + insert_after child raises ValueError
- replace parent + remove child raises ValueError
- conflict across multiple overlays raises ValueError
- sibling anchors (not ancestor/descendant) pass
- single anchor passes
- parent targeted but child not targeted passes

Closes review comment r3596368746 (PR #3557, round 2, cluster 3).

Assisted-by: GitHub Copilot (model: claude-sonnet-4.6, autonomous)
Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

* fix(overlays): fix over-broad conflict detection and non-deterministic ID collision

Finding 1.1 — _check_anchor_conflicts was rejecting any ancestor/descendant
anchor pair, including insert-only edits that are perfectly safe. Only
replace/remove on an ancestor can destroy its subtree and make a descendant
anchor unresolvable. Change the signature to accept a dict[str, str]
(anchor → winning operation) and skip the check for insert_after/insert_before.

Finding 1.2 — merge_steps was calling find_step on the already-mutated tree,
so a replacement step that reused a base step ID could be accidentally targeted
by a later edit group (non-deterministic result depending on dict iteration
order). Replace the anchor-group loop with a single-pass _traverse_and_apply
that walks the original tree structure and applies edits as each step is
encountered. Anchors are never re-looked up in a mutated tree.

Design invariant enforced: overlays always apply to the original base tree and
cannot target steps introduced by other overlays. Non-remove edits on non-base
anchors now raise ValueError early.

Also removes apply_edit (no production callers, only tested in isolation) and
its test class — the new traversal inlines the same mechanics without the
find_step round-trip.

Assisted-by: GitHub Copilot (model: claude-sonnet-4.6, autonomous)

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

* fix(overlays): reject ID trailing newlines and reuse existing .yaml path

Fix two input validation bugs in the overlay layer (Group 2 of copilot
review PR #3557):

1. _validate_safe_id in schema.py used re.match() which anchors only at
   the start of the string, so IDs like 'overlay\n' passed validation
   and could produce newline-containing file paths. Changed to fullmatch()
   so the entire string must satisfy the pattern.

2. workflow_overlay_add always wrote <id>.yml without checking whether
   <id>.yaml already existed. Since the resolver loads both extensions,
   this created two active layers whose edits applied twice. Now uses
   the existing _find_overlay_file() to detect a pre-existing file and
   reuse its path, falling back to .yml only for new overlays.

Tests added for both fixes.

Assisted-by: GitHub Copilot (model: claude-sonnet-4.6, autonomous)

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

* fix(overlays): fix display order inversion and wrap file-read errors

Finding group 3 from copilot-review-v2.md:

3.1 — Precedence display inverted (overlays/__init__.py)
collect_all_layers used a single-pass sort by (-priority, source_asc),
which placed the *losing* equal-priority source first in the display
while claiming "highest first". Fix: two-pass stable sort — source
descending then priority descending — so the actual winner (last applied
by the composer) rises to the top of the display.

3.2 — Unwrapped file-read errors (overlays/layer_sources.py)
Only yaml.YAMLError was caught around path.read_text(), so an
unreadable or non-UTF-8 overlay produced a raw traceback. Fix: widen
the except clause to (yaml.YAMLError, OSError, UnicodeDecodeError),
matching the pattern used throughout catalog.py.

Tests:
- test_workflow_resolve_equal_priority_winner_shown_first: verifies
  project:zzz (the winner) appears before project:aaa in workflow resolve
  output when both overlays share the same priority.
- tests/workflows/test_overlay_layer_sources.py (new): OSError and
  non-UTF-8 bytes both produce OverlayLoadError, not raw tracebacks.

Assisted-by: GitHub Copilot (model: claude-sonnet-4.6, autonomous)

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

* fix: rename misleading overlay test

Assisted-by: GitHub Copilot (model: gpt-5.3-codex, autonomous)

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

* fix: remove EOF blank line in overlay resolver

Assisted-by: GitHub Copilot (model: gpt-5.3-codex, autonomous)

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

* Potential fix for pull request finding

Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com>

* fix: handle overlay read and enumeration errors

Assisted-by: GitHub Copilot (model: gpt-5.3-codex, autonomous)

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

* fix(overlays): validate resolver workflow IDs

Reject unsafe and reserved workflow IDs before overlay or base sources construct paths, preventing traversal through resolver and engine fallback paths.

Assisted-by: GitHub Copilot (model: GPT-5.6 Sol, autonomous)

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

* Potential fix for pull request finding

Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com>

* fix(overlays): drop _remove_sources_recursively from remove branch

In _traverse_and_apply, the remove branch called _remove_sources_recursively
to clean up attribution entries for the deleted step.  This was inherited from
the old apply_edit loop (c70a5d6) where it was needed because the sources dict
was queried exhaustively.

In the current single-pass design, _build_attribution only traverses the result
list, so stale sources entries for removed steps are never read.  The cleanup
call is therefore unnecessary — and actively harmful when another overlay has
replaced a different step with a new step that reuses the same ID: the pop
clobbers the replacement's attribution entry, causing workflow resolve to report
the surviving step as 'unknown'.

Fix: simply remove the _remove_sources_recursively call from the remove branch.
Add an attribution assertion to the existing reused-ID regression test to catch
this case.

Fixes: r3604242050 (Copilot review finding)

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>
Assisted-by: GitHub Copilot (model: claude-sonnet-4.6, autonomous)

* Fix CLI overlay ID validation anchoring

Use fullmatch for CLI workflow/overlay ID validation so trailing newlines are rejected consistently with manifest validation.

Add regression coverage for newline-suffixed workflow and overlay IDs in overlay set-priority.

Assisted-by: GitHub Copilot (model: gpt-5.3-codex, autonomous)

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

* fix(workflows): validate workflow_id in layer sources before path construction

ProjectOverlaySource.collect() and BaseWorkflowSource.collect() joined
workflow_id directly onto storage paths without validation, enabling
path traversal (e.g. '../../outside') when called outside the
WorkflowResolver.

Add _validate_workflow_id() to layer_sources.py — mirrors the same
_SAFE_ID_PATTERN / _RESERVED_WORKFLOW_IDS check used by WorkflowResolver
in overlays/__init__.py — and call it at the top of both collect()
methods before any path is constructed.

Adds parametrised tests covering unsafe IDs and verifying no filesystem
access occurs for an invalid ID.

Closes review finding r3604772700.

Assisted-by: GitHub Copilot (model: claude-sonnet-4.6, autonomous)

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

* fix(workflows): align layer source validation with _safe_workflow_id_dir

Plan §4.1 requires that Workflow-ID-Validierung, Symlink-/Containment-
Prüfungen and Fehlerübersetzung must not diverge between workflow
management and the overlay resolver.

My previous fix added ID pattern + reserved-name validation to both
collect() methods but was missing the containment step and the
BaseWorkflowSource directory/file checks that _safe_workflow_id_dir
performs.

Changes:
- Add _ensure_contained_dir(path, root) to layer_sources.py — pure
  domain mirror of overlays/_commands.py::_ensure_contained_dir that
  raises OverlayLoadError instead of typer.Exit
- ProjectOverlaySource.collect(): replace two inline symlink/dir checks
  with _ensure_contained_dir(workflow_overlay_dir, self.overlays_dir),
  adding the missing resolve().relative_to() containment step
- BaseWorkflowSource.collect(): add _ensure_contained_dir on the
  workflow directory, and add workflow.yml symlink check before is_file()

The same logic now lives in three places (workflow CLI, overlay CLI,
layer sources). The DRY extraction to workflows/_validation.py is
deferred to PR 3 per plan §4.1.

Tests: add containment and symlink tests for both sources.

Assisted-by: GitHub Copilot (model: claude-sonnet-4.6, autonomous)

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

* Potential fix for pull request finding

Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com>

* fix(overlays): resolve identity from manifest field, not filename

Align overlay identity resolution with the project-wide convention:
presets use preset.id, extensions use extension.id, workflows use
workflow.id, and workflow steps use step.type_key. Overlays must
derive identity from the manifest id field, not the filename.

Rewrite _find_overlay_file() to scan all YAML files in the overlay
directory and match on the manifest id field, fixing the bug where
enable/disable/remove/set-priority failed when filename != manifest id.

Closes: PR #3557 discussion r3605010197

Assisted-by: opencode-go/qwen3.7-max (autonomous)

* Potential fix for pull request finding

Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com>

* fix(workflows): make validation behavior consistent across YAML loading paths

Address PR #3557 review finding r3607632921:

- Wrap yaml.YAMLError → ValueError in from_yaml() and from_string() so
  malformed YAML matches the documented exception contract
- Add except ValueError to workflow_info to handle composition errors
  cleanly instead of crashing with a raw traceback
- Remove validate_workflow() from compose() so the resolver path is
  parse-only like all other YAML loading mechanisms; callers validate
  explicitly via engine.validate()
- Update test to reflect new behavior: resolve() returns composed
  definition, caller validates separately

Assisted-by: opencode-go/qwen3.7-max (autonomous)

* fix(overlays): list disabled overlays in management view

Keep disabled overlays visible in workflow overlay list while leaving resolution behavior unchanged.

- add an include_disabled opt-in to overlay source/resolver collection
- use include_disabled=True for workflow overlay list
- add regression tests for list visibility and default filtering

Assisted-by: GitHub Copilot (model: GPT-5.4, autonomous)
Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

* Potential fix for pull request finding

Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com>

* docs: align overlay extends and resolver contract

Assisted-by: GitHub Copilot (model: GPT-5.3-Codex, autonomous)

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

* fix: use atomic write for overlay file updates to prevent hard-link attack

Replace in-place write_text() calls in workflow_overlay_add() and
_update_overlay_field() with the same mkstemp → write → os.replace()
pattern used by the workflow installer (_stage_workflow_file /
_commit_workflow_file / _discard_staged_workflow_file).

The prior code rejected symlinks and validated path containment, but a
hard-linked destination file passes both checks while sharing an inode
with an external file. write_text() would then truncate and overwrite
that external inode. The atomic staging approach never opens the
existing destination for writing, eliminating the hard-link vector.

Fixes findings r3608669512 and r3608669517 on PR #3557.

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>
Assisted-by: GitHub Copilot (model: claude-sonnet-4.6, supervised)

* fix(composer): preserve invalid base definition instead of coercing steps to []

When 'steps' is not a list, returning early with the unmodified
WorkflowDefinition lets validate_workflow surface the proper error
("'steps' must be a list.") to the caller. The previous silent
coercion to [] masked the validation error entirely.

Fixes: https://github.com/github/spec-kit/pull/3557#discussion_r3608669506

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>
Assisted-by: GitHub Copilot (model: claude-sonnet-4.6, supervised)

* fix: align workflow overlay priority semantics

Assisted-by: GitHub Copilot (model: GPT-5.6 Terra, autonomous)

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

* fix: validate overlay priority presentation

Assisted-by: GitHub Copilot (model: GPT-5.6 Terra, autonomous)

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

* fix: catch OverflowError in normalize_priority for float infinity values

YAML values like `priority: .inf` parse to float('inf'), causing
int() to raise OverflowError. This broke validate_overlay_yaml()'s
'validation never raises' contract. Adding OverflowError to the
except clause makes it fall back to the default priority (10),
consistent with other invalid value handling.

Assisted-by: GitHub Copilot (model: claude-sonnet-4.6, autonomous)
Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

---------

Co-authored-by: Markus <markus@example.com>
Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>
Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com>
2026-07-21 08:35:25 -05:00
Roland Huss
6688b447b7 feat(workflows): expose workflow source directory to steps (#3469)
* feat(workflows): expose workflow source directory to steps (#3467)

Propagate WorkflowDefinition.source_path to steps via
{{ context.workflow_dir }} in template expressions and
SPECKIT_WORKFLOW_DIR env var for shell steps. The original
source directory is persisted in state.json so resume
restores the correct value instead of the run-directory copy path.

Closes #3467

Assisted-By: 🤖 Claude Code

* fix: apply bot review suggestions (#2)

Applied fixes from bot review comments:
- Comment #3563319058: prevent stale SPECKIT_WORKFLOW_DIR leak from parent env
- Comment #3563319094: use cross-platform Python one-liner instead of printenv
- Comment #3563319103: add monkeypatch.delenv for deterministic env var test
- Comment #3563319116: same env leak fix as #3563319058

Assisted-By: 🤖 Claude Code

* fix: use YAML single-quotes and forward-slash paths for Windows CI (#2)

sys.executable on Windows returns backslash paths (D:\a\...) which YAML
double-quoted strings interpret as escape sequences. Switch to
single-quoted YAML strings and normalize paths with replace("\\", "/").

Assisted-By: 🤖 Claude Code

* fix: resolve workflow_dir to absolute path and add installed-by-ID test (#3469)

Applied fixes from bot review comments:
- Comment #3563382853: resolve source_path before taking parent to ensure absolute paths
- Comment #3563382864: add test for installed-by-ID workflow_dir semantics

Assisted-By: 🤖 Claude Code

* docs: document context.workflow_dir and SPECKIT_WORKFLOW_DIR

Add reference documentation for the new workflow_dir runtime value in
both workflows/README.md and docs/reference/workflows.md so workflow
authors can discover the feature and its semantics.

Assisted-By: 🤖 Claude Code

* fix: clarify installed workflow_dir is an absolute path (#3469)

The documentation for context.workflow_dir described the installed-by-ID
case as ".specify/workflows/<id>/" which appears relative, contradicting
the "resolved absolute path" semantics. Clarified that it is the absolute
path to the installation directory.

Assisted-By: 🤖 Claude Code

* fix: apply bot review suggestions (#3469)

Applied fixes from bot review comments:
- Comment #3580005128: Quote sys.executable in shell step env var test
- Comment #3580005174: Quote sys.executable in no-env-var test

Assisted-By: 🤖 Claude Code

* fix: apply bot review suggestions (#3469)

Applied fixes from bot review comments:
- Comment #3587146944: Quote interpolated workflow_dir path in example

Assisted-By: 🤖 Claude Code
2026-07-15 08:09:35 -05:00
Ali jawwad
fb076a38b8 fix(workflows): fan-out max_concurrency .inf falls back to sequential, not crash (#3521)
_run_fan_out coerces max_concurrency with int() inside except (TypeError,
ValueError). int(float('inf')) raises OverflowError, which is not in that tuple,
so a YAML 'max_concurrency: .inf' crashed the whole run with an uncaught
OverflowError instead of the documented 'cannot be coerced -> sequential'
fallback. Add OverflowError to the except tuple (nan already coerced via
ValueError).

Extends the existing invalid-value parametrization with float('inf')/nan (fails
before on inf: OverflowError; passes after: sequential, all items in order).

Co-authored-by: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
2026-07-15 08:06:03 -05:00
Marsel Safin
d7b6626218 feat(workflows): align workflow CLI with extension command surface (#3419)
* feat(workflows): align workflow CLI with extension command surface

Adds the missing workflow commands and flags so the workflow CLI
matches the extension/preset pattern: add --dev and --from, search
--author, update, enable and disable. Disabled workflows are blocked
from running and marked in list output.

Fixes #2342

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

* fix(workflows): preserve disabled state on update, guard corrupted registry entries

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

* fix(workflows): guard list against corrupted registry entries, re-raise typer.Exit in catalog install

workflow list now skips non-dict registry entries with a warning instead
of crashing, matching update/enable/disable. The broad except in
_install_workflow_from_catalog no longer swallows typer.Exit, so precise
errors like the non-HTTPS redirect message are not duplicated.

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

* fix(workflows): escape rich markup in id-mismatch errors and validate --from source early

The two id-mismatch error paths interpolated repr() into Rich markup, so
a stray bracket in a user typo could be parsed as markup. Route both
through rich.markup.escape.

`workflow add <source> --from <url>` also validated the source only
after downloading. Validate it up front so a URL/path/typo fails
without a network fetch.

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

* fix(workflows): escape rich markup in list output and catalog install errors, isolate update failures

workflow list now escapes id/name/version/description before printing,
matching how extensions render user-editable fields. The catalog install
helper computes safe_wf_id once and uses it for every early error path
plus the final failure message.

workflow update wraps _safe_workflow_id_dir and the backup read inside
the try/except typer.Exit block so an unsafe id in a corrupted registry
fails that one workflow and the rest continue.

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

* fix(workflows): escape rich markup in --from download exception message

Matches how the catalog install path escapes exception strings.

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

* fix(workflows): catch OSError in per-workflow update loop and make restore best-effort

Transient FS errors (perms, disk full) from backup read or write no
longer abort the whole update run. The restore is wrapped in its own
try/except so a failed write only warns, and the offending workflow
is reported via 'Failed to update' like other per-workflow failures.

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

* fix(workflows): escape rich markup in search output

workflow search now escapes catalog-derived name/id/version/description/
tags before printing, matching extension search and workflow list.

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

* fix: escape workflow validation errors before Rich output

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

* fix(workflows): escape remaining unescaped Rich markup paths

Covers the last few review threads not yet addressed:
- Escape yaml.YAMLError text in the local workflow add install path
  (matches the already-escaped download/catalog paths).
- Escape the non---dev local directory fallback's "No workflow.yml
  found in <path>" message (the --dev branch already escaped it).
- Escape the redirected final_url in the --from non-HTTPS redirect
  error (IPv6 literals like http://[::1]/... are legal and contain
  brackets).
- Escape the "Downloaded workflow is invalid" exception message in
  _install_workflow_from_catalog, matching the sibling catalog-install
  exception handler a few lines above it.

Adds regression tests for each in TestWorkflowCliAlignment, following
the existing escaping-test pattern in this class.

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

* fix(workflows): escape workflow name/id in install success messages

Workflow names and ids come from user-controlled YAML or external catalog
data; printing them unescaped lets bracket characters be interpreted as
Rich tags. Escape them in the add/catalog-install success messages and the
remaining catalog error paths, matching the rest of the output hardening.

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

* fix(workflows): fail cleanly on unparseable catalog install URLs

urlparse raises ValueError on e.g. an unbalanced IPv6 literal before the
invalid-URL branch is reached; on workflow update that also bypassed the
per-workflow handler and aborted the whole command. Convert the parse
failure into a clean error so add fails cleanly and update skips just the
affected workflow.

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

* fix(workflows): reject catalog updates whose downloaded version mismatches

The update path never verified the downloaded workflow carries the catalog
version that triggered the update, so a stale or misconfigured URL could
report success while leaving the old version installed or downgrading it.
Pass the expected version into the install helper and fail the update when
the downloaded definition does not match.

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

* fix(workflows): validate workflow ID in run command and document new CLI flags

Path-equivalent spellings like "align-wf/" previously bypassed the
registry disabled check because the engine normalizes the path while the
registry matches the raw string. workflow run now validates non-file
sources against the workflow ID pattern before lookup.

Also updates docs/reference/workflows.md with --dev/--from install
options, update/enable/disable commands, and the search --author flag.

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

* fix(workflows): enforce disabled state for direct paths to installed workflows

Running the installed copy's YAML directly (specify workflow run
.specify/workflows/align-wf/workflow.yml) skipped the registry check.
File sources resolving inside .specify/workflows/<id>/ now map back to
the workflow ID and refuse to run while disabled.

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

* fix(workflows): reject explicit empty --from URL instead of catalog fallback

'workflow add foo --from ""' fell through 'from_url or ...' to a
catalog install. Distinguish None from empty string so explicit values
stay on the URL-validation path and fail closed.

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

* fix(workflows): registry rollback on save failure, consistent disabled check, honest update summary

- WorkflowRegistry.add now rolls back its in-memory mutation when save()
  raises, so a later successful save cannot persist metadata for a
  failed update alongside the restored YAML backup.
- workflow run uses the same truthiness check for 'enabled' as list and
  disable, so malformed values like 0 or null refuse to run.
- workflow update reports 'No workflows were eligible for update' when
  every target was skipped instead of claiming all are up to date.

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

* fix(workflows): guard non-string catalog URL and keep enable/disable rollback intact

- A truthy non-string catalog url (e.g. 123) reached urlparse and raised
  AttributeError, escaping the clean error path; validate it is a string.
- enable/disable mutated the live registry entry before add(), so add's
  rollback snapshot captured the already-toggled object; pass a fresh
  mapping instead.

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

* fix(workflows): tolerate non-dict registry entries in add and clarify test docstrings

A corrupted-but-parseable registry entry (e.g. a string value) crashed
WorkflowRegistry.add with AttributeError on existing.get. Guard the
non-dict case while still restoring the original raw value on rollback.

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

* fix(workflows): atomic registry save and accurate mixed-target update summary

- save() wrote the registry with open('w'), so a failed dump truncated
  the file and the next load reset every entry. Write to a sibling temp
  file and os.replace into place.
- workflow update no longer claims all workflows are up to date when
  some targets were skipped; it reports checked-only status with a
  skipped count.

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

* fix(workflows): exclusive temp file for registry save and cwd-independent disabled guard

- save() now uses tempfile.mkstemp in the workflows dir (matching the
  engine's atomic writer), so a pre-created symlink at a predictable
  .tmp path cannot redirect the write and concurrent processes cannot
  collide.
- The direct-path disabled guard derives the owning project from the
  resolved file path instead of the caller's cwd, so running an
  installed workflow's YAML from outside the project still refuses when
  disabled.

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

* fix(workflows): symlink guards and shape validation in workflow registry, dev-dir file check

- WorkflowRegistry now mirrors StepRegistry: _load refuses symlinked
  parents/registry file and normalizes a non-dict workflows field;
  save() rejects symlinked paths before writing.
- workflow add --dev requires workflow.yml to be a regular file so a
  directory named workflow.yml gets the documented CLI error instead of
  an uncaught IsADirectoryError.

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

* fix(workflows): validate download redirects before following them

All three workflow download sites (add --from, catalog install, step
install) passed no redirect_validator to open_url, so an HTTPS URL
redirecting to cleartext HTTP issued the insecure request before the
post-hoc geturl() check reported it. Shared validator now rejects
non-HTTPS redirects (loopback HTTP allowed) pre-follow, matching the
preset download path.

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

* test(workflows): accept redirect_validator kwarg in step-add open_url fakes

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

* fix(workflows): guard directory-shaped workflow.yml and unreadable registry

- workflow add's plain local-path fallback (no --dev) checked wf_file.exists()
  before installing, so a directory literally named workflow.yml passed the
  guard and _validate_and_install_local() leaked an uncaught
  IsADirectoryError instead of the documented CLI error. Use is_file(),
  matching the --dev branch's existing guard.
- WorkflowRegistry._load() treated any OSError while reading an existing
  registry the same as corrupted JSON, resetting to an empty in-memory
  registry. A later save() would then silently persist that empty state via
  os.replace, discarding every previously installed workflow entry. Track a
  _load_error flag on OSError-during-read and have save() refuse to write
  when it is set, so a transient I/O failure can no longer overwrite intact
  data on disk.
- docs/reference/workflows.md: document `--from <url>` with its value
  placeholder, matching extensions.md and presets.md.

Assisted-by: GitHub Copilot (model: Claude Sonnet 5, autonomous)
Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

* fix(workflow): rollback registry.remove() and guard OSError at CLI boundaries

Critical: WorkflowRegistry.remove() deleted the in-memory entry then
called save() with no rollback, unlike add(). Combined with
workflow_remove deleting the workflow directory before calling
registry.remove(), a save failure permanently destroyed the workflow's
files, left the on-disk registry still claiming it installed, and
surfaced a raw unhandled OSError with no CLI message.

- WorkflowRegistry.remove() now rolls back the in-memory entry on a
  save() OSError, mirroring add()'s existing rollback pattern.
- workflow_remove persists the registry removal (registry.remove(),
  wrapped in try/except OSError -> clean escaped message) before
  deleting any files, so a save failure never touches the workflow
  directory.

Important sibling paths: workflow add (local/--dev/--from and catalog),
enable, and disable all called registry.add() without catching its
deliberate OSError, so a save failure surfaced either an orphaned
install directory (fresh local/catalog installs) or a raw/unhandled
exception with no clean CLI output.

- _validate_and_install_local (backs local/--dev/--from) now removes
  the freshly created directory on a fresh install, or restores the
  prior workflow.yml bytes on a reinstall-over-existing-local install,
  before raising a clean escaped error.
- _install_workflow_from_catalog wraps the final registry.add() using
  the function's own established convention (rmtree the just-downloaded
  workflow_dir, then a clean escaped error) -- workflow_update's
  existing backup/restore around this function is unaffected.
- workflow_enable/workflow_disable catch registry.add()'s OSError and
  print a clean escaped message instead of leaking the exception.

Added failing-first tests proving each behavior (registry-unit rollback
test, CLI-level remove/add/enable/disable save-failure tests
parametrized where they share one root cause), all confirmed red before
the fix and green after.

Assisted-by: GitHub Copilot (model: Claude Sonnet 5, autonomous)
Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

* fix(workflow): preserve prior catalog install on reinstall registry-save failure

_install_workflow_from_catalog's final registry.add() failure handler
unconditionally rmtree'd workflow_dir. That's safe for a brand-new
install, but plain `workflow add <catalog-id>` also allows re-adding an
already-installed workflow, downloading the new version over the
existing directory first. If registry.add() then failed to save, the
unconditional rmtree deleted the prior working install while the
registry (after its own rollback) still reported it installed -- data
loss with no way back. workflow_update already avoids this via an outer
backup/restore around this function, but plain add has no such caller.

Fix mirrors _validate_and_install_local's existed-before/backup-aware
handling: capture whether workflow_dir existed and back up its
workflow.yml bytes before any download write, then on a registry.add()
OSError, restore those bytes for a reinstall or rmtree only a
brand-new directory. Only one file (workflow.yml) is ever written by
this path, so no further per-file bookkeeping is needed.

Added a failing-first regression: install a catalog workflow, re-add it
with a simulated registry save OSError, and assert a clean error, the
original workflow.yml restored byte-for-byte, and the registry still
reporting the original version installed. Confirmed red (prior file
deleted) before the fix, green after.

Assisted-by: GitHub Copilot (model: Claude Sonnet 5, autonomous)
Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

* fix(workflow): centralize catalog-install cleanup across all failure branches

_install_workflow_from_catalog is new in this PR and has seven failure
branches after the mkdir/download step, each independently rmtree'ing
workflow_dir: redirect-to-non-HTTPS rejection, a generic download
exception, invalid downloaded YAML, a validate_workflow failure, a
workflow-id/catalog-key mismatch, a version mismatch, and (fixed in the
prior commit) a registry.add() OSError. Only the last one had been
special-cased to spare a prior working install on reinstall; the other
six still unconditionally deleted the whole directory, so re-adding an
already-installed catalog workflow and hitting any of those six earlier
failures destroyed the working install even though nothing about it had
actually changed.

Replaced all seven ad hoc rmtree call sites with a single local
_cleanup_failed_install() helper that closes over the existed_before /
prior_workflow_bytes captured once at the top of the function: restore
the prior workflow.yml for a reinstall, or rmtree only a directory that
this attempt itself created. Every failure branch now calls this one
helper, so the fix is structural rather than duplicated, and every
existing error message/exit code is unchanged -- only the cleanup
performed before each message is different.

Added a parametrized regression test covering the four early-failure
trigger points reachable from plain workflow add (redirect rejection,
download exception, invalid YAML, ID mismatch): each installs a catalog
workflow, re-adds it while forcing that specific failure, and asserts a
clean error plus the original workflow.yml surviving byte-for-byte.
Confirmed red against the unfixed code (all four raised FileNotFoundError
reading the deleted file) before applying the helper, green after.

Assisted-by: GitHub Copilot (model: Claude Sonnet 5, autonomous)
Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

* fix(workflow): restore registry entry verbatim on post-removal rmtree failure

workflow_remove now persists registry.remove() before deleting any
files (fixed previously), but if the registry write succeeds and the
subsequent shutil.rmtree(workflow_dir) then fails, the registry was
left claiming the workflow uninstalled while its directory remained on
disk -- an orphaned install with no path back to a clean state.
workflow_step_remove already handles this exact sequencing by capturing
the registry entry before removal and restoring it directly into
registry.data plus save() (bypassing add(), which would stamp a new
updated_at) if the directory removal fails afterwards.

Applied the same pattern to workflow_remove: capture registry_metadata
via registry.get() before registry.remove(), and on an rmtree OSError,
write it straight back into registry.data["workflows"][workflow_id] and
save(), matching workflow_step_remove's restore-failure handling (a
yellow warning, not a hard failure, since the primary error is already
about to be reported). Existing error message and exit behavior for the
rmtree failure are unchanged.

Added a failing-first regression: install a workflow, monkeypatch
shutil.rmtree to raise OSError, and assert a clean existing error
message, the directory remaining (rmtree never actually deleted
anything), and the registry entry restored byte-for-byte identical
(including installed_at/updated_at) -- proving the fix bypasses add()
and doesn't re-stamp timestamps. Confirmed red (registry entry stayed
None) before the fix, green after.

Assisted-by: GitHub Copilot (model: Claude Sonnet 5, autonomous)
Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

* Fix 4 current Copilot review findings on workflow run/registry/install

1. workflow run ownership check followed symlinks via Path.resolve()
   before mapping a direct YAML path back to its installed workflow ID.
   A symlinked .specify/workflows/<id>/workflow.yml resolved outside the
   tree, missed the ownership match entirely, and let the disabled-workflow
   guard be silently skipped while engine.load_workflow still followed the
   symlink. Now maps ownership from a lexically-normalized path (os.path.
   normpath, no symlink following) and explicitly refuses to run if the
   installed <id> directory or workflow.yml leaf is itself a symlink.
   Direct external workflow paths that don't match .specify/workflows/...
   are unaffected.

2. WorkflowRegistry._load() caught a read OSError and silently fell back
   to an empty in-memory registry, only blocking a later save(). Callers
   that only query is_installed()/get()/list() before writing a file
   (e.g. commands/init.py's bundled speckit install, which overwrites
   workflow.yml once is_installed() reports false) could act on that
   false-empty state and destroy real data before ever reaching save().
   _load() now raises OSError immediately so an unreadable registry fails
   closed at construction, before any query or side effect is possible.
   Added _open_workflow_registry() to give every CLI command a consistent
   clean-error boundary around registry construction.

3. _validate_and_install_local's mkdir/copy2 ran before the try/except
   that protected registry.add(); a copy2 failure (e.g. a truncating
   partial write on a reinstall) was not caught at all, so the existing
   backup-restore cleanup never ran and the prior working workflow.yml
   was corrupted with a raw traceback surfaced to the user. mkdir/copy2
   now run inside the same rollback-protected section as registry.add(),
   sharing one _cleanup_failed_install() helper.

4. workflow update's skip message claimed any non-catalog source was
   installed "from a local path or URL", which is wrong for the bundled
   speckit workflow (source: "bundled"). Message is now source-neutral.

Verified all 4 threads are current (not outdated) via GraphQL review
thread query on PR #3419, HEAD 812050a.

Tests: strict TDD per fix (red test proving each bug, minimal production
change, green). tests/test_workflows.py: 474 passed. Full suite: 3976
passed, 110 skipped. ruff check: all checks passed on touched files and
full src tree.

Assisted-by: GitHub Copilot (model: Claude Sonnet 5, autonomous)
Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

* Fix disabled-workflow bypass via symlinked .specify project root

workflow run's ownership check derived registry_root/registered_id from
the lexical path, then checked the id directory and workflow.yml leaf for
symlinks -- but never checked .specify or .specify/workflows themselves
for that derived root. _reject_unsafe_workflow_storage only guards the
cwd's project_root, which can differ from the path-derived registry_root
(a direct path into an unrelated project, or that project's own .specify
being a symlink to an attacker-controlled tree). WorkflowRegistry's own
symlinked-parent handling silently substitutes an empty registry instead
of raising, so a query against it (is_installed/get returning "not
found") is not a safety signal a caller can rely on: with a symlinked
.specify, the disabled check saw no registry entry and let a disabled
workflow run anyway.

Fix: reject an unsafe .specify/.specify-workflows for the actual derived
registry_root before ever consulting the registry, reusing the existing
_reject_unsafe_dir helper already used by _reject_unsafe_workflow_storage.

Red-first end-to-end repro: victim project's .specify symlinked to an
attacker-controlled tree containing a disabled workflow entry, run
invoked with a direct path from an unrelated cwd -- confirmed the
disabled workflow executed (exit 0) before the fix, now refused cleanly.

Tests: tests/test_workflows.py 475 passed. Full suite: 3977 passed, 110
skipped. ruff check: all checks passed.

Assisted-by: GitHub Copilot (model: Claude Sonnet 5, autonomous)
Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

* Fix raw exception leak in bundle remove primitive boundary

remove_bundle() had no exception handling around its component
removal loop, unlike install_bundle() which converts any raw
exception into a clean BundlerError. Since WorkflowRegistry now
fails closed (raises OSError) on an unreadable registry file,
and _WorkflowKindManager.__init__ constructs WorkflowRegistry
with no try/except, an unreadable workflow registry surfaced as
a raw OSError through remove_bundle(). The bundle_remove CLI
command only catches BundlerError, so the raw OSError propagated
uncaught, producing exit_code=1 with empty output instead of a
clean, actionable message.

Wrap remove_bundle()'s component loop in the same
try/except BundlerError: raise / except Exception: raise
BundlerError(...) from exc pattern already used by
install_bundle(), converting any raw exception at this shared
boundary. save_records() remains outside the try block, so a
failure still leaves the bundle's record untouched (no removal
side effects recorded).

Tests:
- tests/integration/test_bundler_install_flow.py::test_remove_converts_raw_installer_exception_to_bundler_error
  (function-level regression: a raw OSError from installer.is_installed
  must become a clean BundlerError, and the bundle record must survive)
- tests/contract/test_bundle_cli.py::test_remove_reports_clean_error_when_primitive_raises_raw_exception
  (CLI-level regression: `specify bundle remove` must print a clean
  actionable message and exit non-zero instead of raw/empty output)

Both tests were confirmed red beforehand: the raw OSError propagated
uncaught out of remove_bundle(), and the CLI-level CliRunner result
showed exit_code=1 with empty output.

Assisted-by: GitHub Copilot (model: Claude Sonnet 5, autonomous)
Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

* Fix 8 current Copilot review findings on registry fail-closed, rollback orphans, backup-read boundaries, and Rich escaping

1. WorkflowRegistry._load(): a symlinked .specify/.specify/workflows
   parent (or a symlinked registry file) silently returned an empty
   registry instead of raising, unlike an unreadable-file read failure.
   A read-only caller (notably the bundler's remove path) querying
   is_installed() before ever writing could conclude an installed
   workflow is absent, skip removing it, then delete the bundle
   record -- leaving the workflow untracked but still on disk. Now
   raises OSError immediately, matching the existing unreadable-file
   fail-closed behavior.

2/8. _validate_and_install_local and _install_workflow_from_catalog:
   when the destination directory already existed but had no prior
   workflow.yml (e.g. a leftover empty dir), existed_before was True
   but there were no backup bytes to restore, so the rollback closure
   did nothing on a later failure -- leaving the newly copied/
   downloaded file behind. Both now unlink the newly created file in
   this case, restoring the pre-existing directory to its prior
   (empty) state.

3/4. Both install paths read the prior workflow.yml bytes (to seed
   the reinstall rollback) *before* any try/except boundary: a read
   failure on the existing file (e.g. a transient permission/FS
   issue) leaked a raw, unescaped OSError instead of the same clean
   CLI error used by every other failure branch in these functions.
   Both reads are now guarded by their own try/except OSError, with
   no writes attempted before the read succeeds (so there is nothing
   to roll back on this specific failure).

5. remove_bundle's exception-conversion message unconditionally
   claimed "No changes were recorded," even though a failure can
   occur after earlier components in the same bundle have already
   been removed from disk (save_records never runs on this path, so
   the record is left claiming the bundle fully installed). The
   message now reports how many components were already removed
   when that happened, instead of asserting no changes occurred.

6/7. workflow_remove's new post-registry-removal directory-failure
   error and its restore-failure warning interpolated workflow_dir
   and the exception values into Rich markup unescaped. A project
   path or OS error message containing Rich-markup-like brackets
   could be parsed as markup and hide/corrupt the displayed text.
   Both now use the existing _escape_markup helper, consistent with
   every other error path in this file.

Tests (tests/test_workflows.py unless noted):
- TestWorkflowRegistry::test_load_symlinked_workflows_dir_fails_closed_not_silently_empty (1)
- TestWorkflowCliAlignment::test_add_dev_fresh_install_into_preexisting_empty_dir_cleans_new_file (2)
- TestWorkflowCliAlignment::test_add_catalog_fresh_install_into_preexisting_empty_dir_cleans_new_file (8)
- TestWorkflowCliAlignment::test_add_dev_reinstall_backup_read_failure_gives_clean_error (3)
- TestWorkflowCliAlignment::test_add_catalog_reinstall_backup_read_failure_gives_clean_error (4)
- tests/integration/test_bundler_install_flow.py::test_remove_partial_failure_message_reflects_partial_state (5)
- TestWorkflowRemoveGuard::test_remove_directory_and_restore_failure_escapes_rich_markup (6/7)

All seven were confirmed red beforehand, matching each thread's
described failure mode exactly (silent empty registry instead of a
raise; orphaned new file left behind; raw unescaped OSError leaking;
a misleading "no changes were recorded" claim; Rich markup consuming
bracketed path/exception text). Also updated
test_registry_save_refuses_symlinked_parent, a pre-existing test that
asserted the symlinked-parent raise at add()/save() time -- it now
raises at construction instead, per fix #1, so the test was adjusted
to match without weakening its guarantee (still asserts no writes
occur under the symlinked target).

Assisted-by: GitHub Copilot (model: Claude Sonnet 5, autonomous)
Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

* Fix 3 current Copilot review findings: bookkeeping-aware BundlerError removal, bounded workflow downloads

1. bundle remove: BundlerError raised by the primitive installer itself
   (e.g. from a kind manager) bypassed the partial-removal bookkeeping
   message added previously via a bare `except BundlerError: raise`. Now
   routes through the same detail-construction logic as generic
   exceptions, so a mid-loop BundlerError after an earlier successful
   removal still reports that the project may be partially uninstalled,
   while a zero-removal BundlerError still reports "No components were
   removed." Both preserve the original exception message and chain
   `from exc`.

2/3. workflow add --from and catalog install/update downloads used
   unbounded `response.read()`, buffering the entire server-controlled
   body into memory before any size check, and trusted Content-Length
   alone where checked at all. Added a single shared
   `_read_response_within_limit()` helper reused by both call sites: it
   fails fast on an oversized declared Content-Length, and separately
   enforces the same cap while streaming in 64KiB chunks so a chunked or
   Content-Length-less response cannot bypass the limit by lying about or
   omitting its size. Chose 5 MiB as the cap: workflow YAML definitions
   are small step/metadata text, not binaries, so this is generous
   headroom against a malicious/misbehaving server without affecting any
   legitimate workflow definition. Both call sites already route any
   raised exception through their existing clean-error and rollback
   (`_cleanup_failed_install`) paths, so no additional error-handling
   plumbing was needed.

Tests: extended the shared `_FakeResponse` test helper (and 5 duplicate
per-test FakeResponse classes) to support `.read(amt)` chunked reads with
an internal cursor (backward compatible with existing bare `.read()`
callers) plus header simulation. Added red-first tests for: BundlerError
after partial removal reporting partial state, BundlerError with zero
removals reporting no changes, --from oversized-Content-Length rejection,
--from oversized-streamed-body-without-Content-Length rejection, and the
same two cases for the catalog install path (asserting no orphan
directory/registry mutation on rejection).

tests/integration/test_bundler_install_flow.py: 17 passed
tests/test_workflows.py: 485 passed
tests -q: 3992 passed, 110 skipped
ruff check: clean on all touched files

Assisted-by: GitHub Copilot (model: Claude Sonnet 5, autonomous)
Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

* Fix temp-file leak in workflow add --from and strengthen size-limit test assertions

workflow_add's --from download path opened a NamedTemporaryFile(delete=False)
-- which creates the file on disk immediately -- then wrote the size-limited
response body before assigning `tmp_path`. If `_read_response_within_limit`
raised (oversized declared Content-Length, or an over-cap streamed body with
no/understated Content-Length), the exception propagated out of the `with`
block before `tmp_path` was ever set, so the outer except handler had no
path to clean up: a 0-byte `.yml` temp file was left behind permanently on
every rejected/failed --from download. Fixed by assigning `tmp_path`
immediately after the file is opened (before the size-limited read/write),
and unlinking it in the except branch when set. Normal post-download cleanup
in the existing `finally: tmp_path.unlink(missing_ok=True)` is unchanged.

Verified (not assumed) the catalog install path has no equivalent leak: it
writes the response bytes directly to `workflow_file` inside `workflow_dir`
(no separate temp file), and any read/size-limit failure is already caught
by the existing `except Exception: _cleanup_failed_install()` handler, which
correctly restores a reinstalled file or removes a freshly-created directory.

While investigating, found the previous round's 4 size-limit tests were
false positives: `_read_response_within_limit`'s `max_bytes` parameter had
its default bound to `_MAX_WORKFLOW_YAML_BYTES` at function-definition time,
so monkeypatching the module attribute in tests had no effect on the
function's actual behavior -- the tests were passing because the oversized
mock bodies failed downstream YAML/id validation instead of the size check.
Fixed by resolving `max_bytes` from the module attribute at call time
(default `None`, resolved inside the function body) so tests can actually
override the effective limit, and strengthened all 4 tests' assertions to
match the specific size-limit error text (whitespace-collapsed to tolerate
Rich's line-wrapping), so they now prove the real code path fires.

Tests: added 2 red-first regression tests (oversized-streamed-body and
oversized-Content-Length --from downloads leave no leftover temp file,
verified against a scratch tempfile.tempdir), confirmed red (real 0-byte
file found) before the fix and green after. Strengthened the pre-existing
4 --from/catalog size-limit tests to assert on the actual error message
instead of generic exit-code/non-empty-output checks.

tests/test_workflows.py: 487 passed
tests -k bundler: 186 passed
tests -q: 3994 passed, 110 skipped
ruff check: clean on all touched files

Assisted-by: GitHub Copilot (model: Claude Sonnet 5, autonomous)
Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

* Harden workflow install/remove transactions with atomic staging

Addresses 5 Copilot review findings on HEAD b8269c8, all centered on
transaction integrity around workflow install/remove/registry writes,
following the atomic_write_json pattern already used in _utils.py:

1. WorkflowRegistry.save() now preserves the existing registry file's
   mode (e.g. 0640/0644) across a save instead of silently downgrading
   it to mkstemp's 0600 default; a brand-new registry still gets the
   secure 0600 default.

2. workflow_remove now stages the install directory out of the way via
   an atomic rename *before* the registry write, rather than deleting
   it directly with shutil.rmtree after the registry already claims it
   removed. This closes a real data-integrity gap: a partially-failed
   rmtree could no longer leave a damaged directory re-marked
   "installed" by the old manual restore-after-rmtree-failure code
   (now deleted -- it's structurally impossible to need it). A
   registry-write failure renames the staged directory back
   (guarded, with an explicit warning if the restore-back rename
   itself fails); a registry-write success is durable, so a later
   failure to delete the staged directory is now a warning (exit 0),
   not a contradictory "Error: Failed to remove" (exit 1) that used to
   claim failure while the registry already recorded success.

3. Local (--dev/--from/plain path) and catalog install/reinstall now
   write new content to a same-directory staging file and commit it
   onto the destination workflow.yml via a single atomic swap, instead
   of writing/downloading directly into the destination file. A prior
   file (reinstall) is renamed aside rather than overwritten in place,
   so it can be restored via rename -- never a content rewrite -- if
   registry.add() subsequently fails; a rollback failure is now
   explicitly reported as a warning instead of escaping unguarded and
   masking the original clean error. This also removes the need to
   read the prior file's bytes into memory before installing (that
   read-before-write step and its failure mode are now unreachable),
   and both local and catalog installs share the same four small
   helpers (_stage_workflow_file / _commit_workflow_file /
   _discard_staged_workflow_file / _rollback_committed_workflow_file,
   plus guarded wrappers) rather than duplicating the logic.

4. Updated a stale comment (workflow_run's ownership-guard rationale)
   that still described WorkflowRegistry._load() as silently
   substituting an empty registry; it now fails closed by raising
   OSError, which the comment now states plainly.

Tests: rewrote the two workflow_remove tests whose assertions encoded
the old (incoherent) rmtree-then-restore contract to instead prove the
new stage-then-commit contract (post-registry-success cleanup failure
is a warning+exit 0; pre-registry-success stage-restore failure is
guarded and escapes markup correctly). Rewrote the local/catalog
"backup read failure" tests, which tested a step the new design no
longer performs, into "restore-rename failure" tests proving the new
guarded rollback boundary. Added registry file-mode preservation tests.
All other existing install/remove/reinstall tests (save-failure
cleanup, pre-existing-empty-dir handling, early-failure-during-
reinstall parametrized cases, Rich markup escaping) continue to pass
unmodified against the new implementation.

Verified via GraphQL that all 5 threads are current (not outdated/
resolved) before fixing. Full suite: 3996 passed, 110 skipped. Ruff
clean on all touched files.

Assisted-by: GitHub Copilot (model: Claude Sonnet 5, autonomous)
Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

* Discard reinstall backup file after registry.add() succeeds

_commit_workflow_file() renames a prior workflow.yml aside to
workflow.yml.bak so it can be restored if registry.add() subsequently
fails. Neither the local install/reinstall path nor the catalog
install/reinstall path ever cleaned up that backup after a successful
registry.add() -- every successful reinstall permanently left a
workflow.yml.bak sibling, which later reinstalls would silently
overwrite/re-orphan.

Add a shared _discard_committed_backup_file() helper, called from both
success paths right after registry.add() durably succeeds (and before
the final "installed" message, preserving output ordering). A fresh
install (backup_file is None) is a no-op. A cleanup failure is reported
as a warning (exit 0), not a failure, since the install itself already
succeeded -- consistent with workflow_remove's post-commit cleanup
warning semantics.

Add red-first regression tests proving: (1) successful local reinstall
leaves no workflow.yml.bak sibling, (2) successful catalog reinstall
leaves no workflow.yml.bak sibling, (3) a cleanup failure on the backup
file after a successful reinstall reports a warning and still exits 0
with the registry correctly reflecting the new install.

Assisted-by: GitHub Copilot (model: Claude Sonnet 5, autonomous)
Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

* Clean up freshly-created dest_dir when staging mkstemp fails

_stage_workflow_file() does dest_dir.mkdir(parents=True, exist_ok=True)
then tempfile.mkstemp(dir=dest_dir, ...). For a fresh install (no prior
directory), if mkdir succeeds but mkstemp then raises (disk
full/EMFILE/quota), the exception previously propagated straight past
both the local-install and catalog-install call sites without any
cleanup, leaving the newly-created empty workflow directory orphaned
on disk with no error indicating why.

Fix at the shared _stage_workflow_file() boundary instead of duplicating
cleanup at each call site: track whether this call created dest_dir: on
a mkstemp failure, remove that directory via a guarded rmdir (never a
broad rmtree, so any concurrently written content would be left
untouched) before re-raising the original OSError unchanged. A
pre-existing (reinstall) dest_dir is never touched by this cleanup,
and a cleanup failure is reported as its own warning without masking
the original error.

Add red-first regression tests proving: a fresh local install (--dev,
plain local path, --from) and a fresh catalog install both clean up the
orphaned directory on a simulated mkstemp failure, and a reinstall over
a pre-existing directory is left untouched by the same failure.

Assisted-by: GitHub Copilot (model: Claude Sonnet 5, autonomous)
Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

* Fix installed-workflow ownership/disabled bypass and resume enforcement

Address 3 current Copilot review findings on the disabled-workflow guard
in `workflow run`/`workflow resume`:

- The lexical `.specify/workflows/<id>` ownership scan stopped at the
  first match scanning from the start of the path. A nested project
  living beneath an outer installed workflow's own directory tree (reusing
  the same segment names) was attributed to the wrong (outer) workflow
  and ID, gating the run on an unrelated workflow's disabled state.
  `_scan_for_workflow_owner` now scans from the end so the nearest
  (innermost) owner always wins.

- A path with no `.specify/workflows` segments of its own (e.g.
  `/tmp/alias.yml`) that is itself a symlink resolving *into* installed
  storage bypassed the disabled check entirely, since only the raw
  lexical path was inspected. `_resolve_installed_workflow_ownership` now
  additionally resolves the real path when the lexical scan finds no
  owner and re-runs the same scan against it, so an outward-pointing
  alias into a disabled workflow is caught too. Genuinely standalone
  external files (no symlink anywhere on the path) are unaffected.

- `workflow resume` bypassed the disabled check altogether: engine.resume()
  replays a persisted run directly from disk with no registry awareness.
  RunState now optionally persists `installed_workflow_id` and
  `installed_registry_root` at run start (set by workflow_run when the
  source resolved to an installed ID); `workflow_resume` pre-loads the
  run state and re-checks the registry's *current* disabled state before
  calling engine.resume(), mirroring workflow_run's own guard. Both new
  fields default to None via RunState.load()'s `.get()`, so runs from a
  direct/non-installed source, and any run persisted before this schema
  addition, resume exactly as before.

The ownership-mapping logic (previously inlined in workflow_run) is
extracted into `_resolve_installed_workflow_ownership` /
`_scan_for_workflow_owner` so both the lexical and resolved-path cases
share the same scan and the existing inward-symlink-component refusal.

Assisted-by: GitHub Copilot (model: Claude Sonnet 5, autonomous)
Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

* Guard --from temp cleanup; drop redundant update rollback; mark POSIX-only tests

Two more current Copilot review findings, both in workflow_add/update:

- `workflow add --from`'s `finally: tmp_path.unlink(missing_ok=True)` ran
  unguarded after `_validate_and_install_local` had already committed the
  file and registry entry (success) or already raised its own clean
  `typer.Exit` (failure). An OSError from that cleanup unlink would
  surface as an unhandled failure even though the install itself
  succeeded. It is now wrapped in try/except OSError, printing a neutral
  warning that doesn't claim success or failure (the finally runs on both
  outcomes) instead of propagating.

- `workflow_update`'s per-item loop performed its own outer backup
  (`wf_file.read_bytes()`) and restore (`wf_file.write_bytes(backup)`)
  around `_install_workflow_from_catalog`, which is itself fully
  transactional (staged download, atomic rename-based commit, its own
  rollback on registry failure) and never leaves a raw OSError or a
  partially-written workflow.yml. The outer restore was therefore dead
  weight for its stated purpose, and — being an unguarded byte-level
  write — was itself an unnecessary place a second failure could truncate
  an already-safely-preserved file. Removed; the loop now only records
  success/failure.

Also marks 3 registry-save file-mode tests
(`test_registry_save_preserves_existing_file_mode`,
`test_registry_save_on_new_registry_uses_secure_default_mode`,
`test_registry_save_failure_preserves_file_on_disk`) as POSIX-only via
the repo's existing `skipif(sys.platform == "win32", ...)` pattern, since
they assert exact POSIX permission bits that don't hold on Windows.

Assisted-by: GitHub Copilot (model: Claude Sonnet 5, autonomous)
Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

* Report possible partial changes on zero-removed bundle removal failure

The final Copilot review finding: `remove_bundle`'s zero-removed-components
error message claimed "No components were removed." even when the failing
installer component may have deleted files before raising -- prior review
rounds already established that DefaultPrimitiveInstaller's removal paths
are not atomic and can leave partial filesystem changes despite raising
before `result.uninstalled` is populated. The zero-count message is now a
conservative caution ("...but the failing component may have made partial
changes before raising, so the project may be partially uninstalled.")
instead of an unconditional claim of no side effects. The >0-removed path
(which already reports the confirmed partial list) is unchanged.

Assisted-by: GitHub Copilot (model: Claude Sonnet 5, autonomous)
Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

* Fix workflow resume disabled-check bypass after project move/rename

RunState.installed_registry_root previously persisted the creation-time
absolute project path unconditionally whenever a run belonged to an
installed workflow. After the whole project directory was renamed or
moved, workflow_resume would open a WorkflowRegistry at that now
nonexistent path, get back an empty/default registry, and silently skip
the disabled-workflow check -- a paused run for a disabled workflow could
be resumed successfully from the new location.

Fix persists installed_registry_root only when the owning root genuinely
differs from the current project_root (true cross-project direct-file-
source invocations). The common same-project case now persists None and
is re-derived from the live project_root at resume time via a new
_resolve_run_owner_root() helper, which also falls back to project_root
if a stored root no longer exists on disk -- covering both the common
case transparently surviving project moves and the cross-project case
degrading safely if its owner project vanishes, rather than silently
skipping the disabled check.

Backward compatible: state files missing the new fields, and states with
a still-existing distinct cross-project root, behave unchanged.

Added regression tests:
- resume blocked after project moved then disabled at new location
- resume still works after project moved while workflow stays enabled
- cross-project registry root is still correctly honored when it exists
- resume falls back to current project's registry when a stored
  cross-project root no longer exists

Assisted-by: GitHub Copilot (model: Claude Sonnet 5, autonomous)
Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

* Fix silenced cleanup failures and malformed run-state type validation

Four fixes from Copilot review on HEAD 4f24735:

1. _discard_staged_workflow_file's fresh-install directory removal used
   shutil.rmtree(dest_dir, ignore_errors=True), so a genuine cleanup
   failure there could never reach _safe_discard_staged_workflow_file's
   warning -- an orphaned directory was left behind with zero report.
   Now removes only if dest_dir still exists and lets a real OSError
   propagate to the existing safe wrapper, which warns while the
   already-printed original install error remains primary.

2. _rollback_committed_workflow_file's fresh-install directory removal
   (post registry.add() failure) had the same ignore_errors=True gap;
   fixed identically so _safe_rollback_committed_workflow_file's warning
   can actually fire.

3. In the --from download-failure branch, tmp_path.unlink(missing_ok=
   True) was unguarded: if it raised (e.g. read-only tempdir), it
   replaced the original "Failed to download workflow" error with a raw
   unhandled OSError instead of a clean typer.Exit. Now guarded exactly
   like the later post-install finally cleanup: a cleanup failure prints
   a warning and the original download error is still reported cleanly.

4. RunState.load() trusted installed_workflow_id/installed_registry_root
   straight out of state.json with no type validation. A malformed value
   (int/list/dict/bool instead of str-or-null) would crash deep inside
   _resolve_run_owner_root or the registry lookup (TypeError building a
   Path, unhashable dict/list as a mapping key) instead of failing
   cleanly. Both fields are now validated as str | None during load,
   raising a clear ValueError that workflow_resume's existing ValueError
   boundary already converts into a clean CLI error with no traceback.
   Valid values (including the empty-string fallback already handled by
   _resolve_run_owner_root) continue to load unchanged.

Added red-first regression tests for each: staged-discard cleanup
warning, rollback cleanup warning, download-failure cleanup-vs-original-
error precedence, and parameterized malformed/valid run-state field
coverage.

Assisted-by: GitHub Copilot (model: Claude Sonnet 5, autonomous)
Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

* Add ValueError boundary to workflow status single-run lookup

QUALITY re-review flagged that fa410d3's new RunState.load() type
validation (malformed installed_workflow_id/installed_registry_root
raising ValueError) leaked as a raw unhandled traceback through
`workflow status <run_id>`, which only caught FileNotFoundError.
`workflow resume` already had the matching ValueError boundary.

Adds an `except ValueError as exc: console.print(f"[red]Error:[/red]
{exc}"); raise typer.Exit(1)` clause mirroring resume's exact pattern
(unescaped interpolation, consistent with the existing convention at
every other ValueError boundary in this file). FileNotFoundError
behavior and the no-run-id list-all-runs path are unchanged.

Added parametrized regression covering malformed installed_workflow_id/
installed_registry_root (int/list) via `workflow status`, plus
regressions locking in the unaffected FileNotFoundError and no-run-id
list-path behaviors.

Assisted-by: GitHub Copilot (model: Claude Sonnet 5, autonomous)
Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

* fix: bound workflow step downloads

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

* fix: preserve workflow reinstall state

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

* fix: fail closed on workflow registry state

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

* fix: make workflow installs transactional

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

* fix: close workflow transaction races

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

* fix: clean up failed workflow transactions

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

* fix: clean up workflow removal state

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

* fix: guard workflow update transactions

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

* fix: harden workflow lifecycle edge cases

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

* fix: verify installed workflow ownership

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

* fix: isolate workflow rollback cleanup

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

* fix: preserve unique workflow backups

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

* fix: bind workflow staging to file descriptors

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

* fix: fail closed on corrupt workflow registry

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

* fix: bind workflow ownership and source identity

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

* fix(workflows): harden redirects and Windows tests

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

* fix(workflows): restore staged removals on serialization errors

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

* fix(workflows): preserve state across interrupted writes

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

* fix(workflows): harden resume ownership checks

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

* fix(workflows): validate persisted run state

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

* fix(workflows): validate origin and release metadata

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

---------

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>
2026-07-14 08:03:33 -05:00
Ali jawwad
9d96c62901 fix(workflows): engine loop cap ignores bool max_iterations (#3270)
The while/do-while loop cap guard 'not isinstance(max_iters, int) or
max_iters < 1' does not fall back to the default for a boolean
max_iterations: isinstance(True, int) is True and True < 1 is False. The
loop then runs range(max_iters - 1) == range(True - 1) == range(0),
capping at a single iteration instead of the default 10. Exclude bools,
mirroring the merged while/do-while validators (#3237) and this
function's own continue_on_error bool handling. execute() does not
auto-validate, so this engine guard is the only defence.

Co-authored-by: Claude Opus 4.8 <noreply@anthropic.com>
2026-07-13 09:34:29 -05:00
Marsel Safin
34514fb20a fix(workflows): report validation errors instead of crashing on non-string workflow.yml scalars (#3421)
* fix(workflows): validate scalar types before string operations in workflow validation

YAML parses unquoted scalars like version: 1.0 and id: 123 as
float/int, which crashed validate_workflow and workflow add with raw
tracebacks. Type-check id, name, version and step ids before regex
and string operations so these surface as validation errors. Accept
an unquoted schema_version: 1.0 instead of printing a self-identical
rejection message.

Fixes #3420

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

* fix(workflows): treat falsey non-strings as type errors, not missing fields

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

* fix(workflows): only accept schema_version 1.0 so the error message is accurate

The check also accepted "1" while the error said Expected '1.0'.
Unquoted YAML 1.0 still works via str(); plain 1 is now rejected with
the message that matches.

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

---------

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>
2026-07-10 09:51:19 -05:00
Huy Do
20f430686c feat(workflows): honor max_concurrency in fan-out via a bounded thread pool (#3224)
* feat(workflows): honor max_concurrency in fan-out via a bounded thread pool

* feat(workflows): address review — sliding-window fan-out, locked output, faithful halt

Address the reviewer feedback on the bounded fan-out concurrency:

- Sliding submission window: keep at most `workers` items in flight and stop
  launching new items once the run is halting, instead of submitting all items
  up front (which let the pool keep starting queued work after a halt).
- Faithful halt prefix: attribute a halt to the specific item whose own
  recorded result halted the run (replaying the sequential break condition,
  honoring continue_on_error/aborted), not the shared run status a later
  concurrent item may have flipped. The returned prefix now includes the actual
  halting item, matching the sequential path. An item that fails before
  recording a result (e.g. an unknown step type) is attributed too, since every
  item runs the same template.
- Lock the parent fan-out output mutation: route the post-fan-out
  step_results[...]['output'] update through a new RunState.set_step_output()
  under the run lock, so it cannot race a concurrent save().
- Docstring: describe int() coercion accurately (numeric strings / floats are
  honored; only non-coercible or <= 1 runs sequentially).

Tests: add concurrent halt-includes-halting-item, continue_on_error-does-not-
truncate, and unknown-template-type-matches-sequential coverage; make the
timing test use a monotonic clock with a looser threshold to avoid CI flakiness.

* feat(workflows): address second review pass — concurrency hardening

- append_log: serialize the log_entries append + log.jsonl write under a
  dedicated RunState._log_lock so concurrent fan-out workers can't interleave
  or corrupt log lines (kept separate from the state lock; never nested).
- _run_fan_out.run_item: read the item output back through the item_ctx it
  executed against rather than the outer context closure — clearer and robust
  if StepContext ever stops sharing the steps dict by reference.
- StepBase: document the thread-safety contract — STEP_REGISTRY holds one shared
  instance per type, so concurrent fan-out invokes execute() on the same object;
  implementations must be stateless/thread-safe (the built-ins already are).
- test_concurrency_is_real: prove parallelism deterministically with a
  threading.Barrier (sequential execution can't clear it) instead of a
  wall-clock timing assertion.

* feat(workflows): address review — stamp updated_at under lock, clarify cancel semantics

- RunState.save(): move the updated_at timestamp assignment inside the run lock
  so the timestamp matches the snapshot the thread serializes and concurrent
  savers don't race on it.
- _run_fan_out docstring: clarify that on a halt only not-yet-started items are
  cancelled; items already running finish but their outputs are ignored
  (Future.cancel() can't stop running work, and the pool joins on exit).

* feat(workflows): serialize on_step_start callback under a lock

The concurrent fan-out path invokes _execute_steps from worker threads, which
calls the engine's on_step_start callback (the CLI sets it to a console.print
lambda). Concurrent invocation could interleave/garble progress output. Guard
the call with a WorkflowEngine._callback_lock so callbacks are serialized;
the lock is uncontended for sequential runs.

* feat(workflows): re-raise worker exceptions in-place to preserve traceback

In _run_fan_out's concurrent path, a worker exception was stashed in first_exc
and re-raised after the loop. Re-raise it from within the except block with a
bare `raise` (after cancelling outstanding futures) so the original traceback is
preserved, and drop the now-unneeded first_exc variable. The ThreadPoolExecutor
__exit__ still joins any already-running workers before the exception escapes.

* feat(workflows): lock final fan-out status, drop redundant output write, bound workers

Address third review pass:

- Remove the unlocked `context.steps[step_id]["output"] = …` writes in the
  fan-out parent update. context.steps[step_id] is the same dict object that
  set_step_output() updates under the run lock, so the direct (unsynchronized)
  mutation was redundant.
- Preserve sequential halt semantics under concurrency: a later in-flight item
  could overwrite state.status after the halting item was identified. _run_fan_out
  now derives the halting item's run status (item_halt_status, replacing the bool
  item_halted) and restores it after the pool joins, so the final status is the
  first halting item's outcome.
- Bound the pool: workers = min(max_concurrency, len(items)) and early-return for
  empty items, so a user-controlled max_concurrency can't over-allocate threads.

Add coverage that an earlier PAUSED item's status wins over a later concurrent
FAILED item.

* feat(workflows): avoid unlocked context.steps writes when it aliases step_results

On a resume run, StepContext is built with steps=state.step_results, so the two
direct `context.steps[...] = ...` writes mutated the shared dict outside the run
lock and could race save(). Route both through a new _record_result helper that
mirrors into context.steps only when it is a distinct object (a fresh run) and
otherwise relies solely on record_step_result's locked write.
2026-06-30 08:23:27 -05:00
Huy Do
3036fe6954 fix(workflows): reject a fan-in wait_for that names an unknown step at validation (#3225)
* fix(workflows): reject a fan-in wait_for that names an unknown step at validation

* fix(workflows): reject fan-in wait_for self-reference and non-string entries

Address review feedback on the fan-in wait_for validator:

- A fan-in's own id is added to seen_ids before the wait_for check, so
  `wait_for: [<self>]` passed validation while producing a silent empty
  join at runtime. Reject self-references explicitly.
- Non-string entries (e.g. YAML `wait_for: [123]`) were skipped by the
  isinstance(str) guard and validated even though they can never match a
  real step id. Flag them as wiring errors.

Add coverage for both cases.
2026-06-29 14:52:08 -05:00
Ali jawwad
d378485696 fix(workflows): reject infinite number-input default instead of raising OverflowError (#3199)
WorkflowEngine._coerce_input normalizes a whole-valued number to int via int(value). For an infinite float (e.g. a 'type: number' input with YAML 'default: .inf') int(inf) raises OverflowError, which is not in the except (ValueError, TypeError) tuple. validate_workflow eager-coerces declared defaults and is documented to RETURN a list of errors, but it only catches ValueError -- so the OverflowError escaped and validate_workflow raised instead of reporting, breaking its contract. (NaN already surfaced cleanly because int(nan) raises ValueError.)

Add OverflowError to the except tuple so an infinite default surfaces as the same clean 'expected a number' ValueError as NaN, consistent with the function's existing fail-fast-on-authoring-mistakes design. Finite values (5.0 -> 5, 3.5 -> 3.5) are unaffected.

Co-authored-by: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
2026-06-29 10:05:51 -05:00
Zied Jlassi
f846d6526c fix(workflows): validate requires keys and reject phantom permissions gate (#3079)
* fix(workflows): validate requires keys and reject phantom permissions gate

A workflow's `requires` block was parsed but its keys were never
validated, so a typo or an unsupported key was silently ignored. Most
importantly, authors could write `requires.permissions.shell: true`
expecting a runtime capability gate — but no such gate exists: a `shell`
step always runs with the user's privileges. The declaration gave a
false sense of sandboxing.

`validate_workflow` now accepts only the recognised keys
(`speckit_version`, `integrations`, `tools`, `mcp`) and rejects anything
else, with an explicit error for `requires.permissions` pointing authors
to `gate` steps for approval. Docs and the model comment are updated to
state that `requires` is advisory, not a security boundary.

- Reject non-mapping `requires`, unknown keys, and `requires.permissions`
- Clarify workflows reference + PUBLISHING.md shell-step guidance
- Tests for valid keys, non-mapping, unknown key, and permissions

Signed-off-by: Zied Jlassi <6190550+zied-jlassi@users.noreply.github.com>
Assisted-by: AI

* fix(workflows): address review feedback on requires validation

Follow-up to the review on #3079:

- Guard `requires` validation on `is not None` instead of truthiness so a
  falsy non-mapping value (e.g. `requires: []` or `requires: ''`) is
  reported as an error instead of being silently skipped; `requires:`
  (YAML null) is still treated as an omitted block. Add a regression test.
- Reword the workflows security note so `requires.permissions` is shown
  as rejected/unsupported rather than as a valid example of `requires`.
- Standardize on US spelling (`_RECOGNIZED_REQUIRES_KEYS`, "recognized")
  to match the surrounding code and ease searching.
- Tighten the permissions-rejection test to assert on specific message
  markers (`requires.permissions` and the `gate` guidance) so it fails if
  the validation path or wording drifts.

Assisted-by: AI
Signed-off-by: Zied Jlassi (Architect AI) <6190550+zied-jlassi@users.noreply.github.com>

* fix(workflows): scope requires validation to workflow keys (drop tools/mcp)

tools and mcp belong to the bundle manifest requires schema (bundler/models/manifest.py, resolved in bundler/services/resolver.py), not the workflow requires validated here. Drop them from _RECOGNIZED_REQUIRES_KEYS and revert the PUBLISHING.md claim that this PR had introduced, so workflow requires only recognizes speckit_version and integrations.

This keeps the existing docs accurate and resolves the inline doc-consistency review comments.

Signed-off-by: Zied Jlassi <6190550+zied-jlassi@users.noreply.github.com>

* refactor(workflows): type WorkflowDefinition.requires as Any pre-validation

self.requires holds the raw parsed value, which before validate_workflow()
runs may be a non-mapping (None for a bare 'requires:', a list for
'requires: []', etc.). Annotating it dict[str, Any] was misleading for
editors/type-checkers; use Any and document that validate_workflow() enforces
the mapping shape.

Addresses Copilot review feedback on engine.py.

Signed-off-by: Zied Jlassi <6190550+zied-jlassi@users.noreply.github.com>

* fix(workflows): reject YAML-null requires: as a non-mapping

Address Copilot review: validate requires the same way as inputs. A
bare requires: parses as YAML null and was previously treated as an
omitted block, which is inconsistent with inputs and lets a stray
requires: line be silently ignored.

Drop the is-not-None guard and check isinstance(..., dict) directly: an
omitted block still defaults to {} (valid), but a present-but-non-mapping
value -- YAML null, [] or '' -- is now an authoring error that surfaces.

Tests: add YAML-null rejection + an omitted-is-still-valid guard test.
Signed-off-by: Zied Jlassi <6190550+zied-jlassi@users.noreply.github.com>

---------

Signed-off-by: Zied Jlassi <6190550+zied-jlassi@users.noreply.github.com>
Signed-off-by: Zied Jlassi (Architect AI) <6190550+zied-jlassi@users.noreply.github.com>
2026-06-24 14:49:43 -05:00
Huy Do
f5f76160a3 feat: surface gate detail in the workflow run/resume --json payload (#2965)
* feat: surface gate detail in the workflow run/resume --json payload

A paused run was indistinguishable from any other pause in the
machine-readable outcome, and the gate's prompt/options/choice never
left the human-facing stream. Record each step's type in the run
state's step results (one engine line) and, when the run sits at a
gate, add a gate block (step_id/message/options/choice) to the payload
so orchestrators can drive review gates without parsing stdout.

Reference implementation for the proposal in #2964.

Addresses #2964

* fix(workflow): only surface gate detail in --json when the run is paused

Address review (#2965): _gate_outcome() emitted a gate block whenever current_step_id pointed at a gate step. Since RunState.current_step_id is never cleared on completion, a completed/failed run whose last step was a gate leaked stale gate detail in run/resume/status --json. Guard on status == paused. Also assert CLI success in the _run_json test helper before JSON-parsing, and add direct coverage for the suppression guard.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

* fix(workflows): surface gate block on aborted runs; stabilize message

Address Copilot review:
- `_gate_outcome` now also surfaces the gate block when a run is `aborted`
  by a gate rejection (`on_reject: abort`), not only when `paused`. Abort
  is the only path that sets ABORTED and it leaves current_step_id on the
  gate, so an orchestrator can read the recorded `choice` for the stop.
- Coerce `message` to a string (it may be a non-string YAML literal that
  GateStep only coerces for interpolation) so the JSON schema stays stable.
- Tests: add a CLI-level aborted-path test, a message-coercion test, and
  extend the suppression test to allow `aborted`; share the run helper via
  `_invoke_json` to avoid duplicating the invoke boilerplate.

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

* test(workflows): assert clean exit in gate-abort JSON test

Address Copilot review: the gate-abort test parsed stdout without first
asserting the CLI exited cleanly, so an invoke failure would surface as an
opaque JSON decode error. Route it through `_run_json` (which asserts
exit_code == 0 before parsing) and drop the now-redundant `_invoke_json`
helper — a gate abort emits the payload and returns, so the run exits 0.

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

* fix: use result.output in run-helper assert; document step_data shape

Address Copilot review:
- `_run_json` asserted with `result.stdout` in the message, but under
  `--json` step output is redirected off stdout — the useful diagnostics
  live on `result.output`. Switch the assertion message to `result.output`
  (the JSON parse still reads stdout), matching the other CLI tests.
- `StepContext.steps` documented a 5-key entry shape; the engine now also
  persists `type` and `status`. Update the docstring to the canonical
  7-key shape so step authors/debuggers see the real record.

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

* test(workflows): align gate-abort JSON test with aborted→exit-1

After rebasing onto main, a gate abort now emits the --json payload and
then exits non-zero (`_run_outcome_exit_code` maps aborted → 1, from the
merged exit-code work). Give `_run_json` an `expected_exit` parameter
(default 0) so the abort case asserts exit 1 while the paused/completed
cases stay at 0 — keeping a single shared helper rather than duplicating
the invoke boilerplate.

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

* fix(workflows): backward-compat gate detection + normalize gate options

Address Copilot review:
- A run paused by an older version has no persisted step `type`, so
  `_gate_outcome` would never surface its gate block on resume. Add
  `_is_gate_step`: prefer the `type` field, but when it is absent fall back
  to the gate's unique output signature (`on_reject`, written only by
  GateStep). A record with a different known `type` is still not a gate.
- Normalize `options` to a list of strings (mirroring the `message`
  coercion) so an unvalidated workflow with non-string options can't
  destabilize the JSON schema.
- Tests: options coercion, type-less gate detection, and a type-less
  non-gate negative case.

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

* fix(workflows): normalize non-list gate options to a stable list[str]

Address Copilot review: the prior options normalization only mapped a
`list`, returning the raw value for any other shape (scalar/tuple), which
contradicted the "stable list[str]" intent. Extract `_normalize_gate_options`:
None stays None; list/tuple maps each element through str; any other scalar
becomes a single-element list (a bare string is one option, never iterated
character-by-character). The emitted schema is now always list[str] | None.
Extend the options test to cover list, tuple, bare string, numeric scalar,
and None.

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

* fix(workflows): normalize gate choice to str; portable plain-gate test

Address Copilot review:
- `_gate_outcome` normalized `message` and `options` but passed `choice`
  through as-is; an unvalidated gate can record a non-string `choice`,
  which contradicts the stable-schema rationale. Coerce `choice` to
  `str | None` (None still means "no decision yet"), consistent with the
  other two fields. Adds a focused choice-coercion test.
- The plain (no-gate) test workflow used `run: "true"`, which fails under
  cmd.exe on Windows (ShellStep uses shell=True). Use the cross-platform
  `run: "exit 0"` (matching the exit-code suite's workflows).

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

---------

Co-authored-by: Claude Fable 5 <noreply@anthropic.com>
2026-06-22 07:05:54 -05:00
Copilot
00bff788c9 Add init workflow step to bootstrap projects like specify init (#2838)
* Initial plan

* Add init workflow step to bootstrap projects like `specify init`

* Address review: simplify stderr capture and extract VALID_SCRIPT_TYPES

* Address review: fail fast on non-empty dir, stdout fallback, README force fix

* Populate exit_code/stdout/stderr in non-empty-dir fast-fail

* fix: address three unresolved review comments in InitStep

- Use `with os.scandir(...)` context manager so the iterator is always
  closed even when `any()` short-circuits, preventing file-descriptor
  leaks in long-running workflow runs.
- Guard `os.chdir(prev_cwd)` in the `finally` block with a try/except
  so an `OSError` (e.g. directory deleted) doesn't bypass returning
  the captured `StepResult`.
- Reject non-string `script` values in `validate()` with a clear error
  message, rather than silently passing them through to become
  `--script True` at runtime.

* Potential fix for pull request finding 'Empty except'

Co-authored-by: Copilot Autofix powered by AI <223894421+github-code-quality[bot]@users.noreply.github.com>

* fix: remove no_git and branch_numbering options removed upstream

The --no-git and --branch-numbering flags were removed from `specify init`
on main. Update InitStep to drop these unsupported config fields and fix
tests accordingly.

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

* fix: address review — integration defaults, integration_options, engine-owned dirs

- Apply DEFAULT_INIT_INTEGRATION fallback when neither step config nor
  workflow context provides an integration, so output.integration always
  reflects the actual integration used.
- Add integration_options config field to support --integration-options
  passthrough (required for generic integration and --skills mode).
- Exclude .specify/ from the non-empty directory fast-fail check so that
  here: true works when the engine has already created its run-state
  directory before steps execute.
- Note: mix_stderr=False is not needed — Click 8.2+ captures stderr
  separately by default and the existing try/except handles access.

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

* fix: implicitly add --force when only engine-owned dirs exist

When the workflow engine creates .specify/workflows/runs/ before steps
execute, the directory is technically non-empty. Previously, specify init
would prompt for confirmation (hanging in unattended mode) unless the
user explicitly set force: true. Now the step detects that only
engine-owned directories (.specify/) are present and implicitly adds
--force so init proceeds without user interaction.

Also fixes the test to exercise the implicit-force path rather than
passing force: True explicitly (which bypassed the check entirely).

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

* fix: derive VALID_SCRIPT_TYPES from shared constant, fail fast on OSError, include all resolved fields in output

- Derive VALID_SCRIPT_TYPES from SCRIPT_TYPE_CHOICES in _agent_config
  so the valid set cannot drift from the specify init CLI.
- Fail fast with a clear error when os.scandir() raises OSError (e.g.
  permission denied) instead of silently treating the directory as empty.
- Include preset, force, and ignore_agent_tools in all output dicts
  (both fast-fail and normal paths) for consistent interpolation and
  debugging downstream.

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

* fix: populate stderr from stdout on older Click, fix force comment wording

- When Click does not expose result.stderr (older versions where stderr
  is mixed into stdout), use stdout as stderr on non-zero exit so
  workflows can consistently read steps.<id>.output.stderr for errors.
- Update README inline comment for force: wording to say 'when target
  directory already exists' rather than 'non-empty directory', matching
  the actual specify init behavior for the project: form.

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

* fix: build argv flags before early returns, use any() for dir scan

- Move argv flag-building (--integration, --script, --preset,
  --ignore-agent-tools) before the non-empty-dir and OSError early
  returns so output['argv'] always reflects the complete command.
- --force is appended after the check since it may be set implicitly.
- Replace list comprehension with any() generator expression to
  short-circuit without allocating a full list of DirEntry objects.

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

* fix: only treat .specify as engine-owned when it is a real directory

A file or symlink named .specify should not be excluded from the
non-empty check. Use entry.is_dir(follow_symlinks=False) to ensure
only an actual directory is considered engine-owned content.

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

* fix: guard implicit force for engine dirs only, fix integration fallback order

- Only set implicit --force when engine-owned directories (.specify/)
  are actually present. A completely empty directory no longer gets
  --force added unnecessarily.
- Fix integration resolution precedence: resolve step config expression
  first, then fall back to workflow default (also resolved), then to
  DEFAULT_INIT_INTEGRATION. Previously, a step expression resolving to
  falsy would bypass the workflow default entirely.

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: Manfred Riem <15701806+mnriem@users.noreply.github.com>
Co-authored-by: Copilot Autofix powered by AI <223894421+github-code-quality[bot]@users.noreply.github.com>
Co-authored-by: Manfred Riem <mnriem@users.noreply.github.com>
Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>
2026-06-17 11:46:51 -05:00
Copilot
40d832f90a Allow specify workflow run to execute YAML files without a project (#2825)
* Initial plan

* feat: add --workflow option to init command for post-init workflow execution

* chore: remove unused import in test file

* refactor: allow workflow run without project when given a YAML file path

Instead of adding --workflow to init, make `specify workflow run ./file.yml`
work without requiring a .specify/ project directory. When the source is a
YAML file that exists on disk, cwd is used as the project root. When it's a
workflow ID, the .specify/ project requirement is preserved.

* Handle standalone workflow path edge cases

* Fix USERPROFILE env var portability and docs notation

* Fix workflow YAML path detection to require regular files

* Harden workflow run against unsafe .specify paths

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
2026-06-04 07:09:54 -05:00
Quratulain-bilal
bb2b49d0ae fix(workflows): validate run_id in RunState.load before touching the … (#2813)
* fix(workflows): validate run_id in RunState.load before touching the filesystem

``RunState.load(run_id, project_root)`` interpolates ``run_id`` directly
into ``project_root / ".specify" / "workflows" / "runs" / run_id`` and
then calls ``state_path.exists()`` and ``json.load`` on the result. The
run_id is reachable from user input via ``specify workflow resume
<run_id>`` (CLI argument) and via ``SPECKIT_WORKFLOW_RUN_ID`` (env var
override on the engine's run path), so a value like ``../escape``
turns ``runs_dir`` into ``.specify/workflows/escape/`` and:

  * ``state_path.exists()`` becomes a file-existence oracle for any
    path the process can read.
  * if a ``state.json`` exists at the traversed location (planted by
    a malicious dependency, a misconfigured shared workspace, or an
    older spec-kit version that happened to write there),
    ``json.load`` parses it and the workflow resumes under the
    attacker-chosen ``workflow_id`` / step state.
  * a subsequent ``state.save()`` then writes back to the traversed
    location, persisting the corruption.

``RunState.__init__`` already validates ``run_id`` against
``r'^[a-zA-Z0-9][a-zA-Z0-9_-]*$'`` — but that check runs on
``state_data["run_id"]`` *after* ``load`` has already done the file
lookup, which is too late to prevent the disclosure.

This change extracts the pattern into a class-level constant
``_RUN_ID_PATTERN`` and a single ``_validate_run_id`` classmethod so
``__init__`` and ``load`` cannot drift, then calls the validator at the
top of ``load`` before any path is built. Mirrors the precedent in
``src/specify_cli/agents.py::_ensure_within_directory`` (used at line
437 of that file) which guards extension-install paths against the
same threat model.

Regression tests parametrize 9 traversal vectors (``../escape``,
``..``, ``../../etc/passwd``, ``foo/bar``, ``foo\bar``, ``.hidden``,
``-flag``, ``foo\x00bar``, empty) and plant a malicious ``state.json``
outside ``runs/`` so a missing guard would surface as a successful
load rather than the ambiguous ``FileNotFoundError``. A second test
asserts ``__init__`` and ``load`` reject the same representative
malformed ID, so future changes to one path can't silently drift from
the other.

* test(workflows): exercise RunState.load in shared-validation test, fix __init__ empty-string asymmetry

Copilot's review on this PR pointed out that
test_init_and_load_share_validation claimed to verify both entry
points share the same validation rules but never actually called
RunState.load — only __init__ and the shared
_validate_run_id helper. A regression in load (e.g. someone
deleting the cls._validate_run_id(run_id) call before the path is
built) would slip through even though __init__ and the helper
stayed aligned, defeating the whole point of the test.

Tightening the test surfaced a real asymmetry the previous version was
silently masking:

    self.run_id = run_id or str(uuid.uuid4())[:8]

The truthiness fallback meant RunState(run_id="") silently
substituted a UUID and skipped validation, while
RunState.load("", project_root) correctly rejected the empty
string. The two entry points diverged on the empty-string vector.
That is exactly the drift the test name claimed to defend against —
and the original test missed it.

Changes
-------

* engine.py: __init__ now distinguishes run_id is None
  (caller omitted it → auto-generate UUID) from an empty string
  (caller provided it → must validate like any other value). Both
  paths still flow through _validate_run_id, but only the
  explicit-None case auto-generates.

* test_workflows.py: test_init_and_load_share_validation is
  now parametrized over one representative vector per category from
  test_load_rejects_path_traversal (parent traversal, embedded
  separator, leading non-alphanumeric, empty string) and asserts that
  *all three* entry points — __init__, _validate_run_id, and
  load — reject the same input. Adding load to the assertion
  is the substantive fix Copilot asked for; keeping __init__ and
  the helper alongside it makes any future drift between the three
  immediately observable instead of having to read three separate
  tests.

Verification
------------

pytest tests/test_workflows.py — 168 passed (was 165 before the
parametrize expansion; __init__ empty-string vector would have
failed the new test against the old engine code, confirming the
asymmetry was real).
2026-06-03 14:26:07 -05:00
Huy Do
1732b9b62e feat(workflows): allow resume to accept updated workflow inputs (#2815)
`workflow resume` now accepts `--input key=value` (the same flag and
parsing as `workflow run`, via a shared `_parse_input_values` helper).
Supplied values are merged over the run's persisted inputs and
re-resolved through the existing typed-validation path
(`_resolve_inputs`), so a resumed/re-run step sees the updated inputs
and ill-typed values fail fast. Keys not supplied keep their persisted
values; resuming without `--input` is unchanged. Reference docs updated.

Distinct from #2405 (file-reference inputs at run time): this is about
supplying inputs at resume time, reusing the existing input model.

Closes #2812.

Co-authored-by: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
2026-06-03 12:04:07 -05:00
Huy Do
7bab0568c5 feat(workflows): add continue_on_error step field for non-halting failures (#2663)
* feat(workflows): add continue_on_error step field

Adds an optional `continue_on_error: bool` field on every step.
When set to `true` and the step fails, the engine records the
result (`exit_code`, `stderr` on `steps.<id>.output` plus `status`
as a sibling key on `steps.<id>`) and continues to the next sibling
step instead of halting the run. Downstream `if`, `switch`, or
`gate` steps can then branch on
`{{ steps.<id>.output.exit_code }}` to route the recovery path.

Engine details
--------------
`WorkflowEngine._execute_steps` now consults the step config when a
step returns `StepStatus.FAILED`:

- Gate aborts (`output.aborted`) always halt the run — operator
  decisions take precedence over the flag.
- Otherwise, if `continue_on_error` is the literal `True`, log a
  `step_continue_on_error` event and proceed to the next sibling.
  The runtime check uses identity comparison (`is True`) rather
  than truthiness, so truthy non-bool values like the string
  `"true"` cannot silently change run semantics even if a caller
  bypasses `validate_workflow()`.
- Otherwise, behave as before: log `step_failed`, set
  `RunStatus.FAILED`, and return.

Validation
----------
`_validate_steps` rejects non-bool values for `continue_on_error`.
Coerced strings like `"true"` are not accepted so authoring
mistakes surface at validation time rather than silently changing
run semantics.

Tests
-----
`TestContinueOnError` in `tests/test_workflows.py` (8 tests):
- `test_undeclared_failure_halts_run` — default halt behaviour.
- `test_declared_and_fired_continues_run` — flag + fail → continue.
- `test_declared_but_step_succeeded_is_noop` — flag + success → no-op.
- `test_if_branch_routes_around_failure` — end-to-end recovery.
- `test_gate_abort_still_halts_with_continue_on_error` — abort
  always halts.
- `test_validation_rejects_non_bool_continue_on_error` — `"true"`
  rejected at validation.
- `test_validation_accepts_bool_continue_on_error` — `true`/`false`
  pass cleanly.
- `test_engine_ignores_truthy_non_bool_continue_on_error` —
  defense-in-depth: engine ignores string `"true"` even when
  validation is bypassed.

Rebased onto current upstream/main (post #2664 merge); the new
`TestContinueOnError` class sits immediately after upstream's
`TestContextRunId` so the two feature suites coexist cleanly.

Closes #2591.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

* docs(workflows): restore runtime context section, clarify gate prompt

Two Copilot findings on d0b9e00:

1. The `### Runtime Context` documentation for `{{ context.* }}` was
   lost during the rebase onto current main (the squash dropped the
   anchor where #2664 had added it). Restored under `## Expressions`
   so users can find `context.run_id` semantics and examples.

2. The continue_on_error example gate had message "Retry or skip?"
   but used the default `options: [approve, reject]` with `on_reject:
   skip`, which implied an automatic retry path that gates do not
   provide. Reworded the message to match the actual approve/reject
   semantics and added an explicit note that retry requires either
   custom gate options + downstream branching or a wrapper loop.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

* docs(workflows): clarify continue_on_error scope — returned FAILED only

Copilot finding on d0b9e00:

The README's "Error Handling" intro implied `continue_on_error` covers
"any other runtime error raised during step execution", but the engine
only consults the flag when a step returns `StepResult(status=FAILED, ...)`.
Exceptions raised out of `step_impl.execute()` propagate to
`WorkflowEngine.execute()`, where the catch-all logs `workflow_failed`
and re-raises — the step result is never recorded, and the flag is
never consulted.

Audited the whole PR diff for the same overclaim:

1. workflows/README.md — main fix. Reworded the Error Handling intro to
   "any step that returns StepResult(status=FAILED, ...)" and promoted
   the parenthetical structural-validation note into the Notes block.
   Added a new "Scope: returned failures only" note that names the
   exception path explicitly and tells step authors how to bring the
   flag into scope for exceptional code (catch internally and return
   FAILED with the failure encoded in `output`).

2. tests/test_workflows.py — section comment used "when an executable
   step fails", same ambiguity. Tightened to "when a step returns
   StepResult(status=FAILED, ...)" and added a sentence calling out
   that unhandled exceptions are out of scope.

3. src/specify_cli/workflows/engine.py — already correct ("any step
   that returns FAILED" in the validator comment; "lets the pipeline
   route around the failure" in the execute path). No change.

Engine semantics and test bodies are unchanged. Docs-only.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

* docs(workflows): clarify on_reject:skip semantics — engine returns COMPLETED, not auto-skip

Copilot finding on b8982a7:

The README example's gate message said "reject to skip the rest of this
branch", and the explanatory paragraph claimed [approve, reject] map
to "continue" vs "skip the rest of this branch". The engine does not
implement automatic branch-skipping. `on_reject: skip` returns
`StepStatus.COMPLETED` (gate/__init__.py:65-66); the next sibling step
runs unconditionally unless the author wires a downstream `if` reading
`{{ steps.<gate-id>.output.choice }}`.

Two fixes:

1. Restructured the YAML example so it actually demonstrates the
   manual-branching pattern: added a `recover` if-step after the gate
   that conditions on `steps.review.output.choice == 'approve'`. Now
   the example shows the real workflow author's responsibility instead
   of implying the engine does it.

2. Replaced the trailing paragraph with three precise notes:
   - both gate options return COMPLETED; `on_reject: skip` controls
     abort behaviour only, not sibling-skipping
   - all three `on_reject` values enumerated with their actual engine
     semantics (FAILED+aborted / COMPLETED / PAUSED)
   - the original retry-loop guidance retained as the third bullet

Updated the gate message in the example to match — "reject to leave the
failure recorded and move on" instead of "reject to skip the rest of
this branch".

Audited the whole PR diff for the same overclaim: no other instance.
Engine semantics, validation, and test bodies are unchanged. Docs-only.

161/161 tests/test_workflows.py pass locally.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

* docs(workflows): clarify gate's role — surfaces, doesn't programmatically branch

Audit follow-up to 393ac6b — three sites repeated the same minor
overclaim about gates being one of the "branch on it" step types
alongside `if` and `switch`:

1. workflows/README.md (the "downstream `if`, `switch`, or `gate`
   steps can branch on it" sentence introducing the example)
2. engine.py:236 (validator inline comment)
3. engine.py:657 (execute-path inline comment)

A `gate` step does not have a `condition` or `expression` field — it
only evaluates expressions for `message` and `show_file` (gate/__init__.py:29,36).
Programmatic branching happens in `if`/`switch`; a gate surfaces the
value to a human operator via message interpolation, and the operator's
choice is recorded in `output.choice` for a *subsequent* `if`/`switch`
to route on.

Reworded all three sites consistently: "a downstream `if` or `switch`
can branch on it (or a `gate` can surface it to the operator via
message interpolation)". The README example already demonstrates this
distinction — the gate carries `{{ }}` template variables in its
message and the `recover` if-step downstream is what actually branches
on the choice.

Engine semantics, validation, and test bodies are unchanged. Docs-only
on the README; comment-only on engine.py.

161/161 tests/test_workflows.py pass locally.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

* docs(workflows): use qualified StepStatus.* instead of bare FAILED/COMPLETED/PAUSED

Three Copilot inline comments on workflows/README.md lines 226, 282, 288
flagged that ``StepResult(status=FAILED, ...)`` is not valid Python —
``StepResult.status`` is a ``StepStatus`` enum value, so the
documented form should be ``StepStatus.FAILED``.

Audited the whole PR diff for the same shorthand. The bare unqualified
form appears in three files added/modified by this PR:

1. workflows/README.md (6 sites) — three ``StepResult(status=FAILED, ...)``
   parentheticals, plus the on_reject Notes bullet listing the three
   step statuses (``FAILED``, ``COMPLETED``, ``PAUSED``).

2. tests/test_workflows.py (4 sites) — section header for
   TestContinueOnError, two test-method docstrings, one inline comment
   about a gate's TTY-fallback behaviour.

3. src/specify_cli/workflows/engine.py (1 site) — the validator inline
   comment added in d0b9e00 said "returns FAILED" where the engine
   code itself uses ``StepStatus.FAILED``.

All 11 sites normalised to the qualified ``StepStatus.<name>`` form so
the docs / test docstrings / inline comments match what readers will
actually find in the engine code and the tests. Engine semantics,
validation, and test bodies are unchanged.

161/161 tests/test_workflows.py pass locally.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

---------

Co-authored-by: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
2026-06-02 10:10:07 -05:00
Copilot
cc3d828227 Add support for SPECKIT_WORKFLOW_RUN_ID override (#2742)
* Initial plan

* feat: support SPECKIT_WORKFLOW_RUN_ID override

* docs: clarify run_id env var precedence wording

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
2026-05-29 10:50:00 -05:00
Manfred Riem
616eba6a57 fix: while/do-while loop condition reads stale iteration-0 step output (#2662)
* fix: while/do-while loop condition reads stale iteration-0 step output

After executing namespaced loop body steps, copy each iteration's
results back to the original unprefixed step key so that
evaluate_condition() sees the latest values instead of stale
iteration-0 data.

Fixes #2592

* address review: cross-platform tests, preserve iteration-0 history

- Rewrite shell scripts in tests to use Python via script files
  instead of POSIX syntax, so they pass on Windows CI.
- Snapshot iteration-0 nested-step results under a namespaced key
  (parent:child:0) before the first copy-back overwrite, preserving
  complete per-iteration history for debugging.

* address review: skip copy-back on paused/failed iterations

Move the status check before the copy-back so that partial results
from paused or failed nested steps (e.g., a gate awaiting input)
do not overwrite the unprefixed key. This preserves correct resume
behavior.

* address review: quote paths in test shell commands

Quote both the Python executable and script file paths in the
run: commands to handle spaces in paths on Windows.

* address review: execute loop body with original IDs

Instead of namespacing step IDs for execution and copying results
back, execute the loop body with original (unprefixed) step IDs so
results naturally land at the right keys.  Snapshot previous
iteration results to namespaced keys (parent:child:N) for history
only.

This fixes multi-step loop bodies where step B references step A's
output within the same iteration — previously step B would see
stale data until the copy-back ran after the entire iteration.

* address review: namespaced execution with per-step copy-back

Revert to namespaced step IDs for execution (preserving unique
log entries and state keys per iteration) but copy each step's
result back to the unprefixed key immediately after it completes.

This preserves backward compatibility (same namespaced key format,
same log IDs) while fixing both the condition evaluation bug and
inter-step references within multi-step loop bodies.

* address review: alias after status check, add multi-step body test

- Move per-step aliasing below the PAUSED/FAILED/ABORTED status
  check so partial results from incomplete steps are not aliased
  back to the unprefixed key.
- Add test_while_loop_multi_step_body_inter_step_refs to exercise
  a multi-step loop body where step B reads step A's output within
  the same iteration, verifying per-step aliasing works correctly.

Addresses feedback from @doquanghuy (items 2 & 4) and Copilot
review on commit 9d0a222.

* address review: stable fallback IDs, expression-based inter-step test

- Use enumerate() for stable fallback IDs when loop body steps lack
  an explicit id (step-0, step-1, etc. instead of always step-0).
- Rewrite multi-step body test so step B uses expression
  substitution ({{ steps.step-a.output.stdout }}) instead of
  reading the counter file directly, making it a true regression
  test for per-step aliasing.
2026-05-21 12:25:03 -05:00
Quratulain-bilal
409ec59704 fix(workflow): support integration: auto to follow project's initialized AI (#2421)
* fix(workflow): support integration: auto to follow project's initialized AI

Closes #2406

(squashed)

* fix(workflow): combine JSONDecodeError and UnicodeDecodeError handling

Address Copilot feedback: UnicodeDecodeError can be raised by both
read_text() and json.loads(), so combining the handlers ensures both
cases produce a consistent, clear error message.

* fix(workflows): honor integration_state schema guard and modern state in 'integration: auto'

Three Copilot follow-ups on PR #2421:

1. engine.py:799 — `_load_project_integration` was bypassing the same
   schema guard `_read_integration_json` enforces. It now reads the
   schema field directly, returns None on a future schema (so the
   workflow falls back to the literal 'auto' default rather than
   guessing), and routes through `normalize_integration_state` /
   `default_integration_key` so modern installs that record
   `default_integration` / `installed_integrations` (without the
   legacy top-level `integration` field) resolve correctly.

2. test_workflows.py — added two regression cases:
   - `integration: auto` resolves a modern normalized state file
   - `integration: auto` falls back when the state file declares a
     newer `integration_state_schema` than this CLI supports

3. test_cli.py — added a CLI-level regression for the `UnicodeDecodeError`
   branch in `_read_integration_json` to match the existing
   malformed-JSON coverage.

* refactor(integration): extract shared try_read_integration_json helper

Address Copilot review on PR #2421:

Both `_read_integration_json` (CLI) and `_load_project_integration`
(workflow engine) were parsing `.specify/integration.json` independently,
duplicating the schema guard and risking drift between the two readers.

Extract the parse + schema validation into a single low-level helper
`try_read_integration_json` in `integration_state.py` that returns either
the normalized state or a structured `IntegrationReadError`. Both callers
now delegate to this helper:

- CLI keeps its loud-fail UX: each error kind ("decode", "os",
  "not_object", "schema_too_new") is translated into the existing console
  message + typer.Exit(1).
- Engine keeps its silent fallback: any error simply returns None so
  `integration: auto` falls back to the workflow's literal default.

This eliminates the divergence Copilot flagged without changing observable
behavior for either caller.

* fix(integration): distinguish missing file from non-regular path

Address Copilot review on PR #2421:

`try_read_integration_json` was collapsing two distinct cases into a
single `(None, None)` return:

1. `.specify/integration.json` truly missing — silent fallback is correct.
2. Path exists but is a directory, socket, or other non-regular file —
   this is a misconfiguration the CLI should surface loudly.

Split the check: `exists()` falsey returns `(None, None)`; existing-but-
not-a-regular-file returns `(None, IntegrationReadError(kind="os", ...))`
so the CLI's loud-fail path produces an actionable error while the
engine still treats it as a fallback to the workflow's literal default.

* docs(workflow): clarify version pin, advisory integrations list, enum exemption

- workflow.yml: fix comment that said 0.8.3 was first release with auto
  resolution; the pin is >=0.8.5 so the comment now matches the pin.
- workflow.yml: clarify that requires.integrations.any is an advisory,
  non-exhaustive compatibility hint, not a closed set.
- engine.py: clarify that the auto-sentinel exemption only skips enum
  membership; declared type is still enforced through _coerce_input.

* fix(workflow): resolve auto sentinel for provided values; report stat errors

Two Copilot findings fixed:

1. _resolve_inputs only resolved the ``integration: auto`` sentinel when it
   came from the input default. A caller explicitly providing
   ``{"integration": "auto"}`` (which the workflow prompt advertises as a
   valid value) bypassed _resolve_default and the literal "auto" leaked
   to dispatch. Provided values now go through the same resolution path
   as defaults, and the enum-membership exemption applies in both cases.
   Regression test added.

2. try_read_integration_json used Path.exists() / Path.is_file() as a
   pre-check. Both return False on some OSErrors (e.g. permission errors
   during stat), which silently treated an unreadable-but-present file
   as missing — the engine fell back without warning and the CLI failed
   to surface the loud error. The pre-check is gone: read_text() is
   attempted directly, FileNotFoundError means missing (silent fallback),
   IsADirectoryError and other OSErrors become loud IntegrationReadError.

* fix(workflow): enforce declared type for string inputs, reject bool-as-number

Two Copilot findings fixed:

1. _coerce_input previously coerced/validated only ``number`` and
   ``boolean`` types, so ``type: string`` silently accepted any Python
   value (numbers, lists, dicts). A YAML authoring mistake like
   ``type: string`` + ``default: 5`` slipped through. Strings are now
   required to actually be strings; non-strings raise ValueError, which
   surfaces as an ``invalid default`` error from validate_workflow.

2. ``type: number`` accepted ``default: true`` because ``bool`` is a
   subclass of ``int`` (``float(True) == 1.0``). Bools are now rejected
   explicitly in the number path so the YAML mistake fails fast. The
   boolean path is also tightened to reject non-bool / non-string
   values for symmetry.

Comment on the auto-sentinel enum exemption updated to reflect the
stronger guarantee. Regression tests added for both rejections.

* fix(cli): drop unused normalize_integration_state import to satisfy ruff

CI's `uvx ruff check src/` flagged this as F401: the symbol was imported
under a private alias but never referenced. Tests stay green after
removal.
2026-05-15 16:03:33 -05:00
Copilot
a00e679918 Add workflow engine with catalog system (#2158)
* Initial plan

* Add workflow engine with step registry, expression engine, catalog system, and CLI commands

Agent-Logs-Url: https://github.com/github/spec-kit/sessions/72a7bb5d-071f-4d67-a507-7e1abae2384d

Co-authored-by: mnriem <15701806+mnriem@users.noreply.github.com>

* Add comprehensive tests for workflow engine (94 tests)

Agent-Logs-Url: https://github.com/github/spec-kit/sessions/72a7bb5d-071f-4d67-a507-7e1abae2384d

Co-authored-by: mnriem <15701806+mnriem@users.noreply.github.com>

* Address review feedback: do-while condition preservation and URL scheme validation

Agent-Logs-Url: https://github.com/github/spec-kit/sessions/72a7bb5d-071f-4d67-a507-7e1abae2384d

Co-authored-by: mnriem <15701806+mnriem@users.noreply.github.com>

* Address review feedback, add CLI dispatch, interactive gates, and docs

Review comments (7/7):
- Add explanatory comment to empty except block
- Implement workflow catalog download with cleanup on failure
- Add input type coercion for number/boolean/enum
- Fix example workflow to remove non-existent output references
- Fix while_loop and if_then condition defaults (string 'false' → bool False)
- Fix resume step index tracking with step_offset parameter

CLI dispatch:
- Add build_exec_args() and dispatch_command() to IntegrationBase
- Override for Claude (skills: /speckit-specify), Gemini (-m flag),
  Codex (codex exec), Copilot (--agent speckit.specify)
- CommandStep invokes installed commands by name via integration CLI
- Add PromptStep for arbitrary inline prompts (10th step type)
- Stream CLI output live to terminal (no silent blocking)
- Remove timeout when streaming (user can Ctrl+C)
- Ctrl+C saves state as PAUSED for clean resume

Interactive gates:
- Gate steps prompt [1] approve [2] reject in TTY
- Fall back to PAUSED in non-interactive environments
- Resume re-executes the gate for interactive prompting

Documentation:
- workflows/README.md — user guide
- workflows/ARCHITECTURE.md — internals with Mermaid diagrams
- workflows/PUBLISHING.md — catalog submission guide

Tests: 94 → 122 workflow tests, 1362 total (all passing)

* Fix ruff lint errors: unused imports, f-string placeholders, undefined name

* Address second review: registry-backed validation, shell failures, loop/fan-out execution, URL validation

- VALID_STEP_TYPES now queries STEP_REGISTRY dynamically
- Shell step returns FAILED on non-zero exit code
- Persist workflow YAML in run directory for reliable resume
- Resume loads from run copy, falls back to installed workflow
- Engine iterates while/do-while loops up to max_iterations
- Engine expands fan-out per item with context.item
- HTTPS URL validation for catalog workflow installs (HTTP allowed for localhost)
- Fix catalog merge priority docstring (lower number wins)
- Fix dispatch_command docstring (no build_exec_args_for_command)
- Gate on_reject=retry pauses for re-prompt on resume
- Update docs to 10 step types, add prompt step to tables and README

* Potential fix for pull request finding 'Empty except'

Co-authored-by: Copilot Autofix powered by AI <223894421+github-code-quality[bot]@users.noreply.github.com>

* Address third review: fan-out IDs, catalog guards, shell coercion, docs

- Fan-out generates unique per-item step IDs and collects results
- Catalog merge skips non-dict workflow entries (malformed data guard)
- Shell step coerces run_cmd to str after expression evaluation
- urlopen timeout=30 for catalog workflow installs
- yaml.dump with sort_keys=False, allow_unicode=True for catalog configs
- Document streaming timeout as intentionally unbounded (user Ctrl+C)
- Document --allow-all-tools as required for non-interactive + future enhancement
- Update test docstring and PUBLISHING.md to 10 step types with prompt

* Validate final URL after redirects in catalog fetch

urlopen follows redirects, so validate the response URL against the
same HTTPS/localhost rules to prevent redirect-based downgrade attacks.

* Address fourth review: filter arg eval, tags normalization, install redirect check

- Filter arguments now evaluated via _evaluate_simple_expression() so
  default(42) returns int not string
- Tags normalized: non-list/non-string values handled gracefully
- Install URL redirect validation (same as catalog fetch)
- Remove unused 'skipped' variable in catalog config parsing
- Author 'github' → 'GitHub' in example workflow
- Document nested step resume limitation (re-runs parent step)

* Add explanatory comment to empty except ValueError block

* Address fifth review: expression parsing, fan-out output, URL install, gate options

- Move string literal parsing before operator detection in expressions
  so quoted strings with operators (e.g. 'a in b') are not mis-parsed
- Fan-out: remove max_concurrency from persisted output, fix docstring
  to reflect sequential execution
- workflow add: support URL sources with HTTPS/redirect validation,
  validate workflow ID is non-empty before writing files
- Deduplicate local install logic via _validate_and_install_local()
- Remove 'edit' gate option from speckit workflow (not implemented)

* Add comments to empty except ValueError blocks in URL install

* Address sixth review: operator precedence, fan_in cleanup, registry resilience, docs

- Fix or/and operator precedence (or parsed first = lower precedence)
- Restore context.fan_in after fan-in step completes
- Catch JSONDecodeError in registry load for corrupted files
- Replace print() with on_step_start callback (library-safe)
- Gate validation warns when on_reject set but no reject option
- Shell step: document shell=True security tradeoff
- README: sdd-pipeline → speckit, parallel → sequential for fan-out
- ARCHITECTURE.md: parallel → fan-out/fan-in in diagram

* Address seventh review: string literal before pipe, type annotations, validate on install

- Move string literal check above pipe filter parsing so 'a | b' works
- Fix type annotations: input_values list[str] | None, run_id str | None
- Run validate_workflow() before installing from local path/URL
- Remove duplicate string literal check from expression parser

* Address eighth review: fan-out namespaced IDs, early return, catalog validation

- Fan-out per-item step IDs use _fanout_{step_id}_{base}_{idx} namespace
  to avoid collisions with user-defined step IDs
- Early return after fan-out loop when state is paused/failed/aborted
- Catalog installs parse + validate downloaded YAML before registering,
  using definition metadata instead of catalog entry for registry

* Address ninth review: populate catalog, fix indentation, priority, README

- Add speckit workflow entry to catalog.json so it's discoverable
- Fix shell step output dict indentation
- Catalog add_catalog priority derived from max existing + 1
- README Quick Start clarified with install + local file examples

* Address tenth review: max_iterations validation, catalog config guard, version alignment

- Validate max_iterations is int >= 1 in while and do-while steps
- Guard add_catalog against corrupted config (non-dict/non-list)
- Align speckit_version requirement to >=0.6.1 (current package version)
- Fan-out template validation uses separate seen_ids set to avoid
  false duplication errors with user-defined step IDs

* Address eleventh review: command step fails without CLI, ID mismatch warning, state persistence

- Command step returns FAILED when CLI not installed (was silent COMPLETED)
- Catalog install warns on workflow ID vs catalog key mismatch
- Engine persists state.save() before returning on unknown step type
- Update tests to expect FAILED for command steps without CLI
- Integration tests use shell steps for CLI-independent execution

* Address twelfth review: type annotations, version examples, streaming docs, requires

- Fix workflow_search type annotations (str | None)
- PUBLISHING.md: speckit_version >=0.15.0 → >=0.6.1
- Document that exit_code is captured and referenceable by later steps
- Mark requires as declared-but-not-enforced (planned enhancement)
- Note full stdout/stderr capture as planned enhancement

* Enforce catalog key matches workflow ID (fail instead of warn)

* Bundle speckit workflow: auto-install during specify init

- Add workflows/speckit to pyproject.toml force-include for wheel builds
- Add _locate_bundled_workflow() helper (mirrors _locate_bundled_extension)
- Auto-install speckit workflow during specify init (after git extension)
- Update all integration file inventory tests to expect workflow files

* Address fourteenth review: prompt fails without CLI, resolved step data, fan-out normalization

- PromptStep returns FAILED when CLI not installed (was silent COMPLETED)
- Engine step_data prefers resolved values from step output
- Fan-out normalizes output.results=[] for empty item lists
- subprocess.run inherits stdout/stderr (no explicit sys.stdout)
- Registry tests use issubset for extensibility

* Address fifteenth review: fan_in docstring, gate defaults, validation guards, reserved prefix

- FanInStep docstring: aggregate-only, no blocking semantics
- FanInStep: guard output_config as dict, handle None
- Gate validate: use same default options as execute
- Validate inputs is dict and steps is list before iterating
- Reserve _fanout_ prefix in step ID validation
- PUBLISHING.md: remove unenforced checklist items, add _fanout_ note

* Address sixteenth review: docs regex, fan_in try/finally, hyphenated dot-path keys

- PUBLISHING.md: update ID regex docs to match implementation (single-char OK)
- FanInStep: wrap expression evaluation in try/finally for context.fan_in
- Expression dot-path: allow hyphens in keys before list index (e.g. run-tests[0])

* Make speckit workflow integration-agnostic, document Copilot CLI requirement

- Workflow integration selectable via input (default: claude)
- Each command step uses {{ inputs.integration }} instead of hardcoded copilot
- Copilot docstring documents CLI requirement for workflow dispatch
- Added install_url for Copilot CLI docs

* Address seventeenth review: project checks, catalog robustness

- Add .specify/ project check to workflow run/resume/status/search/info
- remove_catalog validates config shape (dict + list) before indexing
- _fetch_single_catalog validates response is a dict
- _get_merged_workflows raises when all catalogs fail to fetch
- add_catalog guards against non-dict catalog entries in config

* Address eighteenth review: condition coercion, gate abort result, while default, cache guard, resume log

- evaluate_condition treats plain 'false'/'true' strings as booleans
- Gate abort returns StepResult(FAILED) instead of raising exception
  so step output is persisted in state for inspection
- while_loop max_iterations optional (default 10), validation aligned
- Catalog cache fallback catches invalid JSON gracefully
- resume() appends workflow_finished log entry like execute()

* Address nineteenth review: allow-all-tools opt-in, empty catalogs, abort dead code, while docstring

- --allow-all-tools controlled by SPECKIT_ALLOW_ALL_TOOLS env var (default: 1)
  Set to 0 to disable automatic tool approval for Copilot CLI
- Empty catalogs list falls back to built-in defaults (not an error)
- Remove unreachable WorkflowAbortError catches from execute/resume
  (gate abort now returns StepResult(FAILED) instead of raising)
- while_loop docstring updated: max_iterations is optional (default 10)

* Address twentieth review: gate abort maps to ABORTED status, do-while max_iterations optional

- Engine detects output.aborted from gate step and sets RunStatus.ABORTED
  (was unreachable — gate abort returned FAILED but status was always FAILED)
- do-while max_iterations now optional (default 10), aligned with while_loop
- do-while docstring and validation updated accordingly

* Coerce default_options to dict, align bundled workflow ID regex with validator

* Gate validates string options, prompt uses resolved integration, loop normalizes max_iterations

* Use parentId:childId convention for nested step IDs

- Fan-out per-item IDs use parentId:templateId:index (e.g. parallel:impl:0)
- Reserve ':' in user step IDs (validation rejects)
- Replaces _fanout_ prefix with cleaner namespacing
- Expressions like {{ steps.parallel:impl:0.output.file }} work naturally

* Validate workflow version is semantic versioning (X.Y.Z)

* Schema version validation, strict semver, load_workflow docstring, preserve max_concurrency

- Validate schema_version is '1.0' (reject unknown future schemas)
- Strict semver regex: ^\d+\.\d+\.\d+$ (rejects 1.0.0beta etc.)
- load_workflow docstring: 'parsed' not 'validated'
- Keep max_concurrency in fan-out output (was dropped)
- do_while docstring: engine re-evaluates step_config condition
- ARCHITECTURE.md: document nested resume limitation

* Path traversal prevention, loop step ID namespacing

- RunState validates run_id is alphanumeric+hyphens (no path separators)
- workflow_add validates catalog source doesn't escape workflows_dir
- Loop iterations namespace nested step IDs as parentId:childId:iteration
  so multiple iterations don't overwrite each other in context/state

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: mnriem <15701806+mnriem@users.noreply.github.com>
Co-authored-by: Copilot Autofix powered by AI <223894421+github-code-quality[bot]@users.noreply.github.com>
2026-04-14 10:11:56 -05:00