refactor(agent): remove skip_soul context loading path

[GritLs]

Summary

• Remove the skip_soul parameter from build_context_files_prompt().
• Keep SOUL.md loading exclusively in load_soul_md() as the identity layer.
• Update tests and docs so project context assembly no longer suggests a second SOUL.md injection path.

Why

skip_soul was added when SOUL.md moved from the project context block to the primary identity slot in #1922. The main prompt assembly now has load_soul_identity for the real cron use case from #17509, so the helper-level fallback path preserves old mixed context behavior and makes the prompt order harder to understand.

How to test

• .venv/bin/python -m pytest -o addopts='' tests/agent/test_prompt_builder.py::TestBuildContextFilesPrompt tests/run_agent/test_run_agent.py::TestBuildSystemPrompt tests/cron/test_cron_workdir.py::TestRunJobTerminalCwd -q
• .venv/bin/python - <<'PY' ... PY smoke test covering load_soul_md() plus build_context_files_prompt()
• git diff --check

Platforms tested

• macOS 26.4, CPython 3.14.3 via uv-created .venv

Related

• Follow-up cleanup to feat: use SOUL.md as primary agent identity instead of hardcoded default #1922 and fix(cron): keep SOUL.md identity when workdir is unset (#16756) #17509. No separate issue was opened for this refactor.

Cross-platform impact

This is prompt assembly cleanup only. It removes duplicate SOUL.md loading from the context helper and does not add platform-specific behavior.