Add detailed file index and enhance skill documentation for autopilot, decompose, deploy, plan, and research skills. Introduce tests-only mode in decompose skill, clarify required files for deploy and plan skills, and improve prerequisite checks across skills for better user guidance and workflow efficiency.

.cursor/skills/plan/steps/01_artifact-management.md

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+## Artifact Management
+
+### Directory Structure
+
+All artifacts are written directly under DOCUMENT_DIR:
+
+```
+DOCUMENT_DIR/
+├── integration_tests/
+│   ├── environment.md
+│   ├── test_data.md
+│   ├── functional_tests.md
+│   ├── non_functional_tests.md
+│   └── traceability_matrix.md
+├── architecture.md
+├── system-flows.md
+├── data_model.md
+├── deployment/
+│   ├── containerization.md
+│   ├── ci_cd_pipeline.md
+│   ├── environment_strategy.md
+│   ├── observability.md
+│   └── deployment_procedures.md
+├── risk_mitigations.md
+├── risk_mitigations_02.md          (iterative, ## as sequence)
+├── components/
+│   ├── 01_[name]/
+│   │   ├── description.md
+│   │   └── tests.md
+│   ├── 02_[name]/
+│   │   ├── description.md
+│   │   └── tests.md
+│   └── ...
+├── common-helpers/
+│   ├── 01_helper_[name]/
+│   ├── 02_helper_[name]/
+│   └── ...
+├── diagrams/
+│   ├── components.drawio
+│   └── flows/
+│       ├── flow_[name].md          (Mermaid)
+│       └── ...
+└── FINAL_report.md
+```
+
+### Save Timing
+
+| Step | Save immediately after | Filename |
+|------|------------------------|----------|
+| Step 1 | Integration test environment spec | `integration_tests/environment.md` |
+| Step 1 | Integration test data spec | `integration_tests/test_data.md` |
+| Step 1 | Integration functional tests | `integration_tests/functional_tests.md` |
+| Step 1 | Integration non-functional tests | `integration_tests/non_functional_tests.md` |
+| Step 1 | Integration traceability matrix | `integration_tests/traceability_matrix.md` |
+| Step 2 | Architecture analysis complete | `architecture.md` |
+| Step 2 | System flows documented | `system-flows.md` |
+| Step 2 | Data model documented | `data_model.md` |
+| Step 2 | Deployment plan complete | `deployment/` (5 files) |
+| Step 3 | Each component analyzed | `components/[##]_[name]/description.md` |
+| Step 3 | Common helpers generated | `common-helpers/[##]_helper_[name].md` |
+| Step 3 | Diagrams generated | `diagrams/` |
+| Step 4 | Risk assessment complete | `risk_mitigations.md` |
+| Step 5 | Tests written per component | `components/[##]_[name]/tests.md` |
+| Step 6 | Epics created in Jira | Jira via MCP |
+| Final | All steps complete | `FINAL_report.md` |
+
+### Save Principles
+
+1. **Save immediately**: write to disk as soon as a step completes; do not wait until the end
+2. **Incremental updates**: same file can be updated multiple times; append or replace
+3. **Preserve process**: keep all intermediate files even after integration into final report
+4. **Enable recovery**: if interrupted, resume from the last saved artifact (see Resumability)
+
+### Resumability
+
+If DOCUMENT_DIR already contains artifacts:
+
+1. List existing files and match them to the save timing table above
+2. Identify the last completed step based on which artifacts exist
+3. Resume from the next incomplete step
+4. Inform the user which steps are being skipped