Resolve all five codegen hacks; update parse node examples with real responses

[briansrls]

Summary

This PR completes the resolution of all five codegen hacks documented in TODO/TODONE/TODO_hacks.md and TODO/TODO_consolidate_di.md. The primary focus is updating parse node examples across three DAGs to test both real transport responses (with exact output assertions) and skip propagation, plus making dependency injection violations explicit in gist-ops.

Key Changes

1. Parse Node Examples: Real Transport Responses (Hack #2 - FIXED)

All parse node examples now provide realistic transport responses instead of only testing skip propagation:

• bootstrap/graph_mock.rs: parse_scan_result now includes a ShellResponse::ok() example with exact assertions on crate_count and crate_names
• ci/graph_mock.rs:
  • parse_deps_exists — added FileResponse { exists: Some(true) } example
  • parse_codegen_exists — added FileResponse { exists: Some(true) } example
  • parse_codegen_result — added ShellResponse::ok() with skip=false example
  • parse_build — added ShellResponse::ok() with skip=false example
  • parse_test — added ShellResponse::ok() with skip=false example
• lib/llm-ops/src/graph_mock.rs: All four LLM parse nodes (openai, anthropic, code_review, secrets) now include real mock_openai_response() or mock_anthropic_response() REST examples

Each parse node retains its skip propagation example as a second test case, ensuring both paths are covered.

2. Dependency Injection: Make Violations Explicit (Hack #1 Phase 1 - FIXED)

lib/gist-ops/src/lib.rs:

• Removed non-injectable wrapper functions sanitize_branch_for_filename() and generate_gist_filename()
• Consolidated to single injectable variants requiring &FilesystemHandle and SystemTime parameters
• GistOps::PrepareRequest::execute() now explicitly constructs FilesystemHandle and captures SystemTime::now() inline with a comment marking this as a Phase 2 DI violation
• All tests updated to use fixed timestamps, making them fully deterministic
• Updated all test helpers to pass required dependencies explicitly

3. OutputMap Migration (Consolidation §15 - COMPLETED)

Migrated remaining raw HashMap::new() output construction to OutputMap:

• lib/tools/cargo/src/ops.rs: 3 sites in Mockable::mock_outputs()
• lib/tools/deps/src/graph.rs: 2 sites in Mockable::mock_outputs()
• lib/primitives/src/collection.rs: 1 site in SetOp::execute()

Remaining HashMap usage (4 sites in core/ir/src/transport/cli.rs, 2 test helpers) cannot use OutputMap due to dependency constraints.

4. Documentation Updates

• TODO/TODONE/TODO_hacks.md: Marked as ✅ Done; documented all five hacks as resolved
• TODO/TODO_consolidate_di.md: Marked Hack Add SVG viz, test helpers, and makegen scaffold #1 Phase 1 and Hack Add cloud resource + secret modeling with DAG upsert patterns #5 as ✅ FIXED; updated status tracking
• TODO/TODO_dag_environment.md: Checked off Phase 1 items for sanitize_branch_for_filename and generate_gist_filename
• TODO/consolidation.md: Marked OutputMap migration as complete with breakdown of migrated vs. remaining sites

Implementation Details

• ValueExpr pipeline: The value_expr.rs pipeline already supported serializing Value::Response and Value::Request to Rust source; no codegen changes were needed — only the graph_mock examples required updating.
• Deterministic tests: All gist-ops tests now use fixed SystemTime values, eliminating race

https://claude.ai/code/session_017jwfqhevE97hrxHZdk8fGL