[Refactor] Single responsibility principle

[tzanko-matev]

The purpose of the refactor was to split current code into files and functions where each file/function is responsible for a single concern. See the design docs in this commit for details. No tests were touched

File-SRP

• ✅ Step 2 complete: introduced src/logging.rs for one-time logger initialisation and migrated tracing session lifecycle (start_tracing, stop_tracing, is_tracing, flush_tracing, ACTIVE flag) into src/session.rs, with src/lib.rs now limited to PyO3 wiring and re-exports.
• ✅ Step 3 complete: added src/runtime/mod.rs with focused activation, value_encoder, and output_paths submodules; RuntimeTracer now delegates activation gating, value encoding, and writer initialisation through the façade consumed by session.rs.
• ✅ Step 4 complete: introduced src/monitoring/mod.rs for sys.monitoring types/caches and src/monitoring/tracer.rs for the tracer trait plus callback dispatch; rewired lib.rs, session.rs, and runtime/mod.rs, and kept a top-level tracer re-export for API stability.
• ✅ Step 5 complete: split the Python package into dedicated formats.py, session.py, and auto_start.py modules, trimmed api.py to a thin façade, and moved the environment auto-start hook into __init__.py.
• ✅ Step 6 complete: resolved outstanding Rust TODOs (format validation, argv handling, function id stability), expanded module documentation so cargo doc reflects the architecture, and re-ran just test to confirm the refactor remains green.
• ✅ Test baseline: just test (nextest + pytest) passes with the UV cache scoped to the workspace; direct cargo test still requires CPython development symbols.

Function-SRP

Stage 0 – Baseline & Guardrails

• ✅ just test (Rust + Python suites) passes; captured run via the top-level recipe.
• ✅ Generated JSON and binary reference traces from examples/value_capture_all.py; outputs stored in artifacts/stage0/value-capture-json/ and artifacts/stage0/value-capture-binary/.
• ⏳ Summarise current ActivationController behaviour and frame traversal notes for reviewer context.

Stage 1 – Session Start-Up Decomposition

• ✅ Step 1 (Rust): Introduced session::bootstrap helpers and refactored start_tracing to delegate directory validation, format resolution, and program metadata collection. Tests remain green.
• ✅ Step 2 (Python): Extracted _coerce_format, _validate_trace_path, and _normalize_activation_path helpers; added tests covering invalid formats and conflicting paths.

Stage 2 – Frame Inspection & Activation Separation

• ✅ Step 1: Added runtime::frame_inspector::capture_frame to encapsulate frame lookup, locals/globals materialisation, and reference counting; on_line now delegates to the helper while preserving behaviour.
• ✅ Step 2: Extended ActivationController with should_process_event/handle_return_event, updated callbacks to rely on them, and removed direct state juggling from RuntimeTracer.

Stage 3 – Value Capture Layer

• ✅ Step 1: Introduced runtime::value_capture::capture_call_arguments; on_py_start now delegates to it, keeping the function focused on orchestration while reusing frame inspectors.
• ✅ Step 2: Added record_visible_scope helper and refactored on_line to delegate locals/globals registration through it.

Stage 4 – Return Handling & Logging Harmonisation

• ✅ Added runtime::logging::log_event to consolidate callback logging across start, line, and return handlers.
• ✅ Exposed record_return_value in runtime::value_capture and refactored RuntimeTracer::on_py_return to orchestrate activation checks, logging, and value recording.
• ✅ Extended runtime tests with explicit return capture coverage and activation deactivation assertions.

Stage 5 – Cleanup & Regression Sweep

• ✅ Audited runtime modules for obsolete inline comments or TODOs introduced pre-refactor; none remained after helper extraction.
• ✅ Documented the helper module map in design-docs/function-level-srp-refactor-plan.md for contributor onboarding.
• ✅ Re-ran just test (Rust cargo nextest + Python pytest) to confirm post-cleanup parity.

[alehander92]

mostly trusting that it makes sense , i am not very familiar with the current codebase, the design ideas/motivation seems probably good

[tzanko-matev]

I wanted to make the size of each function and each file smaller in order to reduce the necessary context for further changes. But as a side-effect I think it made the code much more readable for myself