feat(federation): establish graph engine foundation

[tcballard]

Purpose

This restores the clean graph-foundation review edge after #463 was merged into an intermediate stack branch while the federation stack itself remained unmerged.

The source trees are unchanged from the previously validated foundation. The commits were rewritten only to add the explicitly authorized DCO trailer and restore linear ancestry.

What this slice contains

• manifest-v2 parsing and bounded multi-parent graph verification
• cycle, divergent-pin, containment, exact-snapshot, and diamond checks
• digest-v2 support
• source-contextual graph composition and qualification
• override-chain and convergence semantics
• closure generation v3 and isolated store/v3 persistence
• exact v1 and no-manifest compatibility
• stable Windows file identity hardening

Stack

• Base: docs(federation): ratify graph-complete v0.29 scope #462 / agent/federation-09-graph-decisions
• Head: agent/federation-10-graph-foundation
• Next: graph-engine activation

This supersedes #463 as the mergeable review edge. Do not merge it independently of the preceding stack. Hosted CI is rerunning on the exact signed head.

[tcballard]

Superseded by #469, which now integrates the exact final intended v0.29.0 tree on current main. This PR is being closed only to remove the obsolete squash-stack edge; its branch and review history remain available.