Record hook degradation status

[azalio]

Summary

• Persist explicit skipped hook reasons for malformed hook input, unsupported tools, and insignificant Bash commands when branch state is safe to update.
• Preserve the non-blocking/no-clobber hook contract for missing or invalid step state.
• Move 2604.017-3 from the active improvement plan to done and capture the reusable hook-input testing rule.

Validation

• pytest tests/test_workflow_context_injector.py tests/test_template_sync.py -v
• pytest tests/test_map_step_runner.py::test_write_run_health_report_creates_report_and_manifest tests/test_artifact_schemas.py::test_validate_run_health_report_schema -v
• make lint
• pytest -m "not slow"
• Generated-project uv run --no-sync mapify init <temp> --no-git --mcp none hook smokes for insignificant Bash and non-string Bash payloads

[Copilot]

Pull request overview

This PR expands workflow hook observability by recording skipped/degraded hook outcomes into branch state when it is safe to do so, so run-health reporting can surface why context injection did not happen.

Changes:

• Adds safe step-state reading and skipped hook status persistence for malformed/unsupported/insignificant hook paths.
• Adds regression tests for skipped Bash, malformed hook input, missing state, invalid state preservation, and non-string Bash payloads.
• Updates README, usage, architecture, roadmap, learned rules, and improvement tracking docs for the new diagnostic signal.

Reviewed changes

Copilot reviewed 11 out of 11 changed files in this pull request and generated 3 comments.

Show a summary per file

File	Description
.claude/hooks/workflow-context-injector.py	Adds degradation-aware state reads and skipped hook status writes.
src/mapify_cli/templates/hooks/workflow-context-injector.py	Syncs the shipped hook template with the source hook changes.
tests/test_workflow_context_injector.py	Adds hook regression coverage for skipped and malformed input paths.
README.md	Documents skipped hook reasons in run health reporting.
docs/USAGE.md	Updates usage docs for run-health hook degradation signals.
docs/ARCHITECTURE.md	Updates architecture description of run-health resiliency signals.
docs/roadmap.md	Marks skipped hook reasons as part of shipped runtime alignment.
docs/learned/testing-strategies.md	Adds a reusable testing rule for untrusted hook JSON fields.
docs/improvement-plan.md	Removes the completed hook degradation coverage plan item.
docs/improvement-loop-log.md	Records implementation and validation of the improvement slice.
docs/improvement-done.md	Adds the completed improvement entry and validation summary.

Comments suppressed due to low confidence (3)

.claude/hooks/workflow-context-injector.py:389

• Non-string Bash commands are malformed hook input, but normalizing them to an empty command makes the persisted skip reason become bash command not significant. That hides the malformed-payload degradation this PR is trying to make auditable; preserve a separate malformed-command reason before falling through to significance checks.

        command = tool_input.get("command", "")
        if not isinstance(command, str):
            command = ""

src/mapify_cli/templates/hooks/workflow-context-injector.py:389

• Non-string Bash commands are malformed hook input, but normalizing them to an empty command makes the persisted skip reason become bash command not significant. That hides the malformed-payload degradation this PR is trying to make auditable; preserve a separate malformed-command reason before falling through to significance checks.

        command = tool_input.get("command", "")
        if not isinstance(command, str):
            command = ""

.claude/hooks/workflow-context-injector.py:398

• The new unsupported-tool skip path is not covered by the updated hook tests; the added tests exercise malformed JSON and Bash skips, but nothing asserts that an unsupported tool with parseable state persists tool not configured for workflow injection without emitting context. Add a regression so this documented behavior does not silently regress.

    if not should_inject:
        reason = "tool not configured for workflow injection"
        if tool_name == "Bash":
            reason = "bash command not significant"
        elif not tool_name:
            reason = "missing tool_name"
        record_skip_if_state_available(branch, reason, tool_name or "unknown")

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