test: Add E2E test skeletons for 26 remaining autonomy scenarios

[jadercorrea]

Summary

Creates E2E test skeletons for all 26 remaining scenarios needed to reach 100% autonomy, as documented in AUTONOMY_GAP_ANALYSIS.md.

What's included

7 new test files (30 test cases total):

High Priority (19 scenarios):

• ✅ complex_modifications_test.go (12 tests): Multi-file refactoring, DB migrations, API changes, security fixes, type system changes, etc.
• ✅ test_generation_test.go (5 tests): Unit tests, integration tests, mocks, snapshots, coverage
• ✅ advanced_validation_test.go (2 tests): Self-review, E2E test creation

Medium Priority (4 scenarios):

• ✅ codebase_understanding_test.go (2 tests): Dependency tracing, doc parsing
• ✅ merge_conflicts_test.go (1 test): Merge conflict resolution

Low Priority (8 scenarios):

• ✅ advanced_git_test.go (5 tests): Rebase, cherry-pick, bisect
• ✅ documentation_test.go (3 tests): README, CHANGELOG, API docs updates

Documentation updates:

• Updated AUTONOMY_GAP_ANALYSIS.md with test file references for each scenario category

Why this matters

We're at 59% autonomy (38/64 scenarios). These 26 scenarios represent the path to 100% autonomy.

Having test skeletons in place provides:

1. Clear roadmap - Each t.Skip() is a TODO with implementation guidance
2. Progress tracking - As capabilities are added, enable corresponding tests
3. Regression prevention - Once enabled, tests stay green
4. Prioritization - Tests organized by priority (HIGH/MED/LOW)

Testing

All test skeletons:

• ✅ Compile successfully
• ✅ Run with go test -tags=e2e
• ✅ All correctly marked as SKIP
• ✅ Include descriptive TODO messages

$ go test -tags=e2e ./tests/e2e/run/... -v -run "TestComplex|TestTest|TestAdvanced|TestMerge|TestDocumentation"
# All 30 tests: PASS (skipped)
# Time: 0.447s

Next steps

After merge, we can systematically tackle scenarios by priority:

1. Phase 7: Complex Code Modifications (12 scenarios) - Biggest impact
2. Phase 8: Test Generation (5 scenarios) - Critical for autonomy
3. Phase 9: Advanced features (codebase understanding, git ops, docs)

Each phase: Implement → Enable tests → Verify → Ship

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Related:

• Builds on 100% MVAA milestone (commit 6edbf12)
• See docs/blog/2025-12-06-100-percent-mvaa.md for context
• Tracks to AUTONOMY_GAP_ANALYSIS.md roadmap