Extract tool and type lookup crud modules

[akwasigroch]

Purpose

app/crud/__init__.py is the crud monolith that apps/backend/AGENTS.md says should only shrink from here. This continues the incremental split started in #2588, #2590, #2591 and #2592, taking the Tool and TypeLookup blocks off the tail of the file.

What Changed

• New crud/tool.py (_TOOL_RELATED_FIELDS, get_tool, get_tools, create_tool, update_tool, delete_tool) and crud/type_lookup.py (get_type_lookup, get_type_lookups, create_type_lookup, update_type_lookup, delete_type_lookup, get_type_lookup_by_name_and_value), moved verbatim from crud/__init__.py.
• 141 lines removed from crud/__init__.py, 998 → 857. No re-exports left behind — the old names are gone from the monolith.
• Callers switched to direct submodule imports: routers/tools.py, routers/type_lookup.py, services/source.py, services/task_notification.py, services/tool/actions.py, services/tool/mcp/config.py, services/tool/rest/config.py, services/tool/rest/health.py and services/tool/rest/jira.py. All but two of those only used the monolith for these entities, so the from rhesis.backend.app import crud import is dropped where it became unused.
• Patch targets and mock variable names updated in tests/backend/services/test_mcp_service.py, test_rest_health.py, test_rest_config.py and test_jira_rest.py — these patch the module attribute by string, so the targets move from ...config.crud to ...config.tool_crud / .type_lookup_crud depending on which entity the block exercises.

This is a pure move: the two new module bodies were diffed byte-for-byte against the removed blocks.

Additional Context

• Tool and TypeLookup ship together because they share caller files (routers/tools.py, services/tool/*); splitting them into two PRs would make the two fight over the same lines.
• services/task_notification.py was reached through a direct name import (from rhesis.backend.app.crud import get_status, get_type_lookup) rather than attribute access, so it does not show up in a crud.get_type_lookup grep. It keeps get_status on the monolith for now.
• get_or_create_type_lookup lives in utils/crud_utils.py and is left alone.
• Two sibling PRs split other blocks of the same file in parallel. They touch different line ranges, but the one that lands second will need a trivial conflict resolution on the task_notification.py import line.
• ruff format also tidied a few pre-existing over-long dict literals and hand-wrapped @patch decorators in test_mcp_service.py and test_rest_config.py as a side effect of formatting those files.

Testing

uv run pytest tests/backend/services/ → 1976 passed, 14 skipped, 1 xfailed.

uv run pytest tests/backend/routes/test_type_lookup.py tests/backend/routes/test_tools_*.py tests/backend/routes/test_source.py → 148 passed, 4 skipped.

Ruff check and format on all 16 touched files are at the pre-change baseline.