feat: use git-backed workspace diffs for memory consolidation

[jif-oai]

Why

This PR make the morpheus agent (memory phase 2) use a git diff to start it's consolidation. The workflow is the following:

1. The agent acquire a lock
2. If .codex/memories does not exist or is not a git root, initialize everything (and make a first empty commit)
3. Update raw_memories.md and rollout_summaries/ as before. Basically we select max N phase 1 memories based on a given policy
4. We use git (gix) to get a diff between the current state of .codex/memories and the last commit.
5. Dump the diff in phase2_workspace_diff.md
6. Spawn morpheus and point it to phase2_workspace_diff.md
7. Wait for morpheus to be done
8. Re-create a new .git and make one single commit on it. We do this because we don't want to preserve history through .git and this is cheap anyway
9. We release the lock
   On top of this, we keep the retry policies etc etc

The goals of this new workflow are:

• Better support of any memory extensions such as chronicle
• Allow the user to manually edit memories and this will be considered by the phase 2 agent

As a follow-up we will need to add support for user's edition while morpheus is running

What Changed

• Added memory workspace helpers that prepare the git baseline, compute the diff, write phase2_workspace_diff.md, and reset the baseline after successful consolidation.
• Updated Phase 2 to sync current inputs into raw_memories.md and rollout_summaries/, prune old extension resources, skip clean workspaces, and run the consolidation subagent only when the workspace has changes.
• Tightened Phase 2 job ownership around long-running consolidation with heartbeats and an ownership check before resetting the baseline.
• Simplified the prompt and state APIs so DB watermarks are bookkeeping, while workspace dirtiness decides whether consolidation work exists.
• Updated the memory pipeline README and tests for workspace diffs, extension-resource cleanup, pollution-driven forgetting, selection ranking, and baseline persistence.

Verification

• Added/updated coverage in core/src/memories/tests.rs, core/src/memories/workspace_tests.rs, state/src/runtime/memories.rs, and core/tests/suite/memories.rs.

[chatgpt-codex-connector]

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