Load a verified checkout's project settings in the full Planner

The full Planner kept the operator's settings in an in-memory manager
with no project scope, so packages a repository installs for itself
(`atomic install -l`, recorded in `.atomic/settings.json`) never loaded,
and their workflows and tools were missing from Planner turns run in that
checkout. Seed the in-memory project scope from the working directory's
`.atomic/settings.json` as trusted project settings, keep both files
unwritten, and reapply Chopin's compaction, summary, and cache overrides.

Assistant-model: Claude Opus 5.5
Assistant-workflow: inline
Assistant-verification: bun test passed: 1749 tests, 2 PostgreSQL skips, 0 fail, including a new full-Planner test that a checkout's project package contributes its tool and skill without writing either settings file
Assistant-verification: bun run types passed: all workspaces
Assistant-verification: bun run ci passed: dprint, oxlint, tokens, type scale, Impeccable baseline
Assistant-verification: local E2E failed before this fix: invoke_planner reached a full Planner whose tools lacked a package installed through the checkout's .atomic/settings.json
User-preference: HARNESS=atomic runs the Planner as a full Atomic session, so a checkout should behave like a local Atomic session in that repository
Co-authored-by: Alex Lavaee <lavaman131@github.com>