fix: close project identity and memory observability issues

[LeXwDeX]

Summary

• fail closed when Git transport/spawn errors prevent project identity discovery
• expose global Memory config initialization, replacement, and declined-write decisions
• keep real Git non-zero exit behavior unchanged

Evidence

• dev Typecheck: passed
• dev CodeQL: passed
• dev Unit Tests (linux): passed
• dev E2E (linux/windows): passed
• full dev CI: https://github.com/LeXwDeX/OpenCode-GraphAgent/actions/runs/31769544719

Closes #239
Closes #240

#238 remains open and is intentionally excluded from this release.