feat(workflows): WorkflowResolver standalone (PR 1) by markuswondrak · Pull Request #3557 · github/spec-kit

markuswondrak · 2026-07-16T08:59:13Z

Summary

This PR implements PR 1 of the workflow-overlays plan: a standalone WorkflowResolver that lets downstream projects extend installed workflows without editing the installed workflow.yml.

It follows the sequencing agreed with @mnriem in Discussion #3473: build the concrete workflow resolver first, keep it independent of PresetResolver, and defer any generic LayerStackResolver abstraction to a later PR.

What's included

WorkflowResolver + StepListComposer (standalone, no shared abstraction)
Pure-function merge engine supporting insert_after, insert_before, replace, remove
Recursive anchor search inside then/else/steps/cases.*/default; fan-out templates excluded as discussed
2-tier layer sources: project overlays + base workflow
workflow overlay add|set-priority|enable|disable|remove|list
workflow resolve <id> for layer attribution
Comprehensive tests under tests/workflows/

Architecture simplification

This PR enforces a clean separation of concerns:

workflow add installs workflows only (no overlay copying)
workflow overlay add installs overlays only (project-local)

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

Review findings resolved

All three review findings from the initial PR review are now resolved:

r3594064677: workflow add no longer copies overlays from all call sites (overlay-copying logic removed entirely)
r3594064705: --priority override now applied before validation, not after (fixes timing issue where valid CLI priority couldn't override missing/invalid file priority)
r3594064726: No stale installed overlays after reinstall (installed overlays tier removed entirely)

Test results

.venv/bin/python -m pytest tests/workflows -q
91 passed

.venv/bin/python -m pytest tests -q
3999 passed, 110 skipped

uv run ruff check src/specify_cli/workflows/overlays src/specify_cli/workflows/_commands.py src/specify_cli/workflows/engine.py tests/workflows
All checks passed!

tests/test_presets.py is untouched and remains green.

Scope notes

PresetResolver is not modified.
The spec/ planning folder is intentionally excluded from this PR.
No new COMPONENT_KINDS entry; overlays are project-local only, matching the simplified 2-tier architecture.

AI assistance disclosure

This implementation was produced with AI assistance (Kimi / opencode-go/kimi-k2.7-code) and has been verified locally by running the full test suite and linting.

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 github#3473 (github#3473) Assisted-by: Kimi (model: opencode-go/kimi-k2.7-code, autonomous)

Copilot

Pull request overview

Implements the standalone WorkflowResolver agreed for PR 1 in Discussion #3473, adding upgrade-safe workflow overlays without modifying PresetResolver.

Changes:

Adds layered workflow composition with recursive step edits and attribution.
Adds overlay management and resolution CLI commands.
Supports shipped overlays, documentation, and comprehensive tests.

Reviewed changes

Copilot reviewed 16 out of 16 changed files in this pull request and generated 8 comments.

Show a summary per file

File	Description
`src/specify_cli/workflows/overlays/__init__.py`	Defines the resolver facade.
`src/specify_cli/workflows/overlays/composer.py`	Composes and validates workflow layers.
`src/specify_cli/workflows/overlays/layer_sources.py`	Loads project, installed, and base layers.
`src/specify_cli/workflows/overlays/merge.py`	Implements step-list merge operations.
`src/specify_cli/workflows/overlays/schema.py`	Defines and validates overlay manifests.
`src/specify_cli/workflows/overlays/_commands.py`	Implements overlay CLI handlers.
`src/specify_cli/workflows/engine.py`	Resolves overlays when loading workflows.
`src/specify_cli/workflows/_commands.py`	Registers commands and installs shipped overlays.
`docs/reference/workflows.md`	Documents overlay behavior and commands.
`tests/workflows/conftest.py`	Adds shared workflow fixtures.
`tests/workflows/test_overlay_commands.py`	Tests overlay CLI operations.
`tests/workflows/test_overlay_composer.py`	Tests composition validation.
`tests/workflows/test_overlay_merge.py`	Tests merge behavior and attribution.
`tests/workflows/test_overlay_schema.py`	Tests manifest formats and validation.
`tests/workflows/test_overlay_security.py`	Tests path-handling protections.
`tests/workflows/test_resolver_integration.py`	Tests end-to-end resolution.

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mnriem · 2026-07-16T12:09:40Z

@markuswondrak Looks like the right direction to me. Now we'll have to get it to the review cycles. So please address Copilot feedback and resolve conflicts

Address PR github#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 github#3557 review comments r3594064534, r3594064563 Assisted-by: opencode-go/qwen3.7-max (autonomous)

- 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 github#3557 review discussion Assisted-by: GitHub Copilot (model: qwen3.7-plus, autonomous)

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 github#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)

Copilot

Pull request overview

Copilot reviewed 16 out of 16 changed files in this pull request and generated 11 comments.

mnriem

Please address Copilot feedback and resolve conflicts

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

…lows.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>

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 github#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>

Resolved conflicts in docs/reference/workflows.md and src/specify_cli/workflows/_commands.py: - docs: kept options table from main + overlay docs from feature branch - _commands.py: adopted main's transactional install refactor Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com> Assisted-by: GitHub Copilot (model: claude-sonnet-4.6, autonomous)

Copilot

Pull request overview

Copilot reviewed 17 out of 17 changed files in this pull request and generated 7 comments.

mnriem · 2026-07-17T13:45:32Z

Please address Copilot feedback

…c 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 two input validation bugs in the overlay layer (Group 2 of copilot review PR github#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>

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>

Assisted-by: GitHub Copilot (model: gpt-5.3-codex, autonomous) Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

Copilot

Pull request overview

Copilot reviewed 18 out of 18 changed files in this pull request and generated 5 comments.

Assisted-by: GitHub Copilot (model: gpt-5.3-codex, autonomous) Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

Copilot

Pull request overview

Copilot reviewed 18 out of 18 changed files in this pull request and generated 4 comments.

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>

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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)

…drak/spec-kit into feat/workflow-overlays

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>

Copilot

Pull request overview

Copilot reviewed 18 out of 18 changed files in this pull request and generated 3 comments.

…struction 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>

mnriem · 2026-07-17T18:43:28Z

Please address Copilot feedback

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>

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…drak/spec-kit into feat/workflow-overlays

Copilot

Pull request overview

Copilot reviewed 18 out of 18 changed files in this pull request and generated 2 comments.

Comments suppressed due to low confidence (2)

src/specify_cli/workflows/overlays/_commands.py:22

re.Pattern.match() accepts a match ending immediately before a trailing newline, so values such as ov1\n pass this CLI guard even though the overlay schema rejects them. The update/remove commands can therefore address filesystem names that are invalid everywhere else. Use fullmatch(), as the schema and existing workflow-ID validation do.

    if not _SAFE_ID_PATTERN.match(id_value):

src/specify_cli/workflows/overlays/layer_sources.py:115

The collector does not enforce unique overlay IDs. If both ov.yml and ov.yaml exist (or differently named files declare the same id), both layers are applied, but update/remove resolves only the first <id> file and can report success while the duplicate remains active. Track IDs while collecting and reject duplicates, or define a single canonical file identity that the CLI also uses.

            layers.append(
                Layer(
                    content=overlay,
                    source=f"project:{overlay.id}",

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 github#3557 discussion r3605010197 Assisted-by: opencode-go/qwen3.7-max (autonomous)

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Copilot

Pull request overview

Copilot reviewed 18 out of 18 changed files in this pull request and generated 1 comment.

Comments suppressed due to low confidence (2)

src/specify_cli/workflows/overlays/_commands.py:22

Use fullmatch() here, as the schema and parent workflow-ID validator do. With match() and this pattern's $, a value such as wf\n is accepted because $ may match before the final newline, allowing an invalid newline-named storage path through the CLI despite the schema's explicit guard.

    if not _SAFE_ID_PATTERN.match(id_value):

src/specify_cli/workflows/engine.py:741

This new call can raise ValueError when a composed workflow or overlay is invalid. workflow_run handles that, but workflow_info calls load_workflow() at src/specify_cli/workflows/_commands.py:2391 and catches only FileNotFoundError, so specify workflow info <id> now leaks an unhandled exception whenever an overlay becomes stale or invalid. Add a clean ValueError path to that caller.

            return resolver.resolve(str(source))

…ng paths Address PR github#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)

…drak/spec-kit into feat/workflow-overlays

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>

Copilot

Pull request overview

Copilot reviewed 18 out of 18 changed files in this pull request and generated 3 comments.

Comments suppressed due to low confidence (2)

src/specify_cli/workflows/engine.py:749

A missing YAML path now falls through to WorkflowResolver, which rejects the dot in missing.yml with ValueError. This changes load_workflow()'s documented missing-file contract from FileNotFoundError to “invalid workflow ID,” so callers can no longer distinguish an absent path from malformed workflow content. Treat any YAML-suffixed source as a path and raise FileNotFoundError before ID resolution when it does not exist.

        # Try as an installed workflow ID, resolving any overlays.
        resolver = WorkflowResolver(self.project_root)
        try:
            return resolver.resolve(str(source))

src/specify_cli/workflows/overlays/layer_sources.py:150

Duplicate manifest IDs are all appended as active resolver layers, but _find_overlay_file() manages only the first sorted match. With aaa.yml and zzz.yml both declaring id: lint, disable, set-priority, or remove can report success after changing aaa.yml while zzz.yml remains active. Enforce unique manifest IDs consistently during loading/addition instead of allowing ambiguous layers.

            overlay, errors = validate_overlay_yaml(data)
            if overlay is None or errors:
                raise OverlayLoadError(path, errors)

+specify workflow overlay list <workflow-id>
+```
+
+Shows enabled overlays for the workflow, ordered by resolver precedence.  Disabled overlays are ignored by the resolver and are not listed.


+| Field | Required | Description |
+| --- | --- | --- |
+| `id` | yes | Identifier for this overlay. Used in `specify workflow overlay *` commands. Must be lowercase letters, digits, and hyphens only; no dots, underscores, path separators, or `overlays`. |
+| `extends` | yes | The workflow id this overlay applies to. Uses the same safe-id format as `id`; `overlays` is reserved. |


+
+        Raises:
+            FileNotFoundError: if the workflow cannot be found.
+            ValueError: if the composed workflow is invalid.


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fix(workflows): harden overlay symlink handling

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fix: rename misleading overlay test

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fix: remove EOF blank line in overlay resolver

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Merge remote-tracking branch 'origin/main' into feat/workflow-overlays

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fix: handle overlay read and enumeration errors

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Merge branch 'feat/workflow-overlays' of https://github.com/markuswon…

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Merge branch 'feat/workflow-overlays' of https://github.com/markuswon…

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Merge branch 'main' into feat/workflow-overlays

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Merge branch 'feat/workflow-overlays' of https://github.com/markuswon…

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…drak/spec-kit into feat/workflow-overlays

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markuswondrak commented Jul 16, 2026 • edited Loading Uh oh! There was an error while loading. Please reload this page.

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Summary

What's included

Architecture simplification

Review findings resolved

Test results

Scope notes

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mnriem commented Jul 16, 2026

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mnriem commented Jul 17, 2026

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markuswondrak commented Jul 16, 2026 •

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