feat(protocol): add append-only integrity invariants and git merge support

[leonardobuares]

Summary

Implements append-only integrity invariants and git merge support for the
shared state logs. Two branches that both appended to JOURNAL.md,
LESSONS.md or decisions.jsonl previously produced a manual conflict, and
a badly resolved one left <<<<<<< markers inside decisions.jsonl,
silently breaking every subsequent boot. Nothing detected any of this.

Closes #5.

Changes

• PROTOCOL_RULES.md (kernel 2.0.1 to 2.1.0): new §P3 Integrity invariants: corrections are new entries (never rewrites of history),
  every append ends with a final newline, structural corruption blocks new
  appends until repaired and logged.
• modules/git-substrate.md (1.2.0 to 1.3.0): new §M-git-7 Merge safety for append-only logs, plus a new .agents/.gitattributes shipping
  merge=union for the three append-only logs. sessions/active_sessions.md
  is deliberately excluded (rows are removed on close; union would resurrect
  them). The section mandates post-merge validation and documents when human
  review is still required.
• validate_state.py: structural checks (conflict markers, missing final
  newline, duplicated top-level header), default targets now include
  JOURNAL.md, LESSONS.md, sessions/active_sessions.md. New pytest
  coverage; pre-commit regex and the state-validation workflow widened.
• CLI: same checks in lead-protocol validate (auto-discover included);
  three corruption/restore scenarios added to test-pack.mjs. Version
  2.0.3 to 2.1.0. Numbered assuming this lands before feat: add first-run setup interview gate (PROTOCOL_RULES §P10) #22/feat(cli): add update command and stop init from overwriting existing installs #26; happy to
  renumber if they land first.
• README.md new "State file integrity" section (per §M-git-3),
  cli/README.md, CHANGELOG.md [2.1.0].

Testing

• pytest .agents/scripts/: 115 passed.
• npm run typecheck passes; npm run test:pack passes end to end,
  including the three new corruption scenarios (fail while corrupted,
  pass after restore).
• Manual experiment: two branches appending to decisions.jsonl under the
  shipped .gitattributes merge cleanly, both entries preserved, no markers.

Checklist

• Code follows project conventions
• Tests added/updated
• Documentation updated
• Protocol files follow defined schemas (state files not modified;
  framework files intentionally changed)

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