Refine coding standards and testing guidelines

- Updated coding rules to emphasize readability, meaningful comments, and maintainability.
- Adjusted test coverage thresholds to 75% for business logic and clarified expectations for test scenarios.
- Enhanced guidelines for handling skipped tests, emphasizing the need for investigation and resolution.
- Introduced a completeness audit for research decomposition to ensure thoroughness in addressing problem dimensions.

Made-with: Cursor

.cursor/skills/test-run/SKILL.md

@@ -102,32 +102,46 @@ After investigating, present:
 - If user picks A → apply fixes, then re-run (loop back to step 2)
 - If user picks B → return failure to the autopilot
 
-**Any test skipped** → this is also a **blocking gate**. Skipped tests mean something is wrong — either with the test, the environment, or the test design. **Never blindly remove a skipped test.** Always investigate the root cause first.
+**Any skipped test** → classify as legitimate or illegitimate before deciding whether to block.
 
-#### Investigation Protocol for Skipped Tests
+#### Legitimate skips (accept and proceed)
 
-For each skipped test:
+The code path genuinely cannot execute on this runner. Acceptable reasons:
 
-1. **Read the test code** — understand what the test is supposed to verify and why it skips.
-2. **Determine the root cause** — why did the skip condition fire?
-   - Is the test environment misconfigured? (e.g., wrong ports, missing env vars, service not started correctly)
-   - Is the test ordering wrong? (e.g., a fixture in an earlier test mutates shared state)
-   - Is a dependency missing? (e.g., package not installed, fixture file absent)
-   - Is the skip condition outdated? (e.g., code was refactored but the skip guard still checks the old behavior)
-   - Is the test fundamentally untestable in the current setup? (e.g., requires Docker restart, different OS, special hardware)
-3. **Try to fix the root cause first** — the goal is to make the test run, not to delete it:
-   - Fix the environment or configuration
-   - Reorder tests or isolate shared state
-   - Install the missing dependency
-   - Update the skip condition to match current behavior
-4. **Only remove as last resort** — if the test truly cannot run in any realistic test environment (e.g., requires hardware not available, duplicates another test with identical assertions), then removal is justified. Document the reasoning.
+- Hardware not physically present (GPU, Apple Neural Engine, sensor, serial device)
+- Operating system mismatch (Darwin-only test on Linux CI, Windows-only test on macOS)
+- Feature-flag-gated test whose feature is intentionally disabled in this environment
+- External service the project deliberately does not control (e.g., a third-party API with no sandbox, and the project has a documented contract test instead)
 
-#### Categorization
+For legitimate skips: verify the skip condition is accurate (the test would run if the hardware/OS were present), verify it has a clear reason string, and proceed.
 
-- **explicit skip (dead code)**: Has `@pytest.mark.skip` — investigate whether the reason in the decorator is still valid. Often these are temporary skips that became permanent by accident.
-- **runtime skip (unreachable)**: `pytest.skip()` fires inside the test body — investigate why the condition always triggers. Often fixable by adjusting test order, environment, or the condition itself.
-- **environment mismatch**: Test assumes a different environment — investigate whether the test environment setup can be fixed.
-- **missing fixture/data**: Data or service not available — investigate whether it can be provided.
+#### Illegitimate skips (BLOCKING — must resolve)
+
+The skip is a workaround for something we can and should fix. NOT acceptable reasons:
+
+- Required service not running (database, message broker, downstream API we control) → fix: bring the service up, add a docker-compose dependency, or add a mock
+- Missing test fixture, seed data, or sample file → fix: provide the data, generate it, or ASK the user for it
+- Missing environment variable or credential → fix: add to `.env.example`, document, ASK user for the value
+- Flaky-test quarantine with no tracking ticket → fix: create the ticket (or replay via leftovers if tracker is down)
+- Inherited skip from a prior refactor that was never cleaned up → fix: clean it up now
+- Test ordering mutates shared state → fix: isolate the state
+
+**Rule of thumb**: if the reason for skipping is "we didn't set something up," that's not a valid skip — set it up. If the reason is "this hardware/OS isn't here," that's valid.
+
+#### Resolution steps for illegitimate skips
+
+1. Classify the skip (read the skip reason and test body)
+2. If the fix is **mechanical** — start a container, install a dep, add a mock, reorder fixtures — attempt it automatically and re-run
+3. If the fix requires **user input** — credentials, sample data, a business decision — BLOCK and ASK
+4. Never silently mark the skip as "accepted" — every illegitimate skip must either be fixed or escalated
+5. Removal is a last resort and requires explicit user approval with documented reasoning
+
+#### Categorization cheatsheet
+
+- **explicit skip (e.g. `@pytest.mark.skip`)**: check whether the reason in the decorator is still valid
+- **conditional skip (e.g. `@pytest.mark.skipif`)**: check whether the condition is accurate and whether we can change the environment to make it false
+- **runtime skip (e.g. `pytest.skip()` in body)**: check why the condition fires — often an ordering or environment bug
+- **missing fixture/data**: treated as illegitimate unless user confirms the data is unavailable
 
 After investigating, present findings: