chore: remove deprecated gitlab_api and polling-related config fields

[Zalfsten]

Summary

Several configuration fields are marked with Field(deprecated=True) in Pydantic v2.
They were kept for backwards compatibility during the migration to GitRepo/Mango-query-based
harvesting but are no longer needed.

Affected items

• Config.gitlab_api — superseded by Config.git_repo; the GitlabApi ArcStore
  implementation (arc_store/gitlab_api.py) and all supporting code can be removed.
• Polling-related fields on HarvestConfig (grace_period_days, auto_mark_deleted)
  — kept as stubs but never used by the harvest pipeline.

Acceptance criteria

• Remove the deprecated fields and their validator guards.
• Delete arc_store/gitlab_api.py and its tests.
• Remove gitlab_api from all example config files and Helm values.
• Update AGENTS.md and architecture docs.
• All unit tests pass; Ruff/mypy/Pylint report no new issues.