Improve agent workflow documentation

[Widthdom]

Summary

• Add README entries for the shared agent guide and Claude Code entry point.
• Cross-link the shared agent guide with the workflow directory README.
• Clarify Codex vs Claude Code guard enforcement and the shared guard core.
• Add a workflow-link checker and precommit reminder for workflow references.
• Make fuzzy suggestion duplicate diagnostics tolerate a closed stderr after the CI failure in SuggestionStore fuzzy duplicate warning can fail on closed stderr #2677.

Validation

• bash .codex/scripts/check-workflow-links.sh
• git diff --check origin/main..HEAD
• dotnet build CodeIndex.sln -c Release -p:UseSharedCompilation=false
• dotnet test CodeIndex.sln -c Release -p:UseSharedCompilation=false
• dotnet test tests/CodeIndex.Tests/CodeIndex.Tests.csproj -c Release --framework net9.0 --filter SuggestionStoreTests -p:UseSharedCompilation=false
• adversarial review round 1: found a blocking issue in the checker command shape
• adversarial review round 2: No blocking/actionable issues found.
• adversarial review after CI fix: No blocking/actionable issues found.

Documentation and changelog

• Updated README.md, AGENT_GUIDE.md, SELF_IMPROVEMENT.md, .codex/workflows/README.md, and .codex/workflows/precommit.md.
• Added changelog fragments:
  • changelog.d/unreleased/1906.fixed.md
  • changelog.d/unreleased/1979.fixed.md
  • changelog.d/unreleased/1995.fixed.md
  • changelog.d/unreleased/1997.fixed.md
  • changelog.d/unreleased/1998.fixed.md
  • changelog.d/unreleased/2677.fixed.md

Follow-up candidates

• None.

Fixes #1998
Fixes #1997
Fixes #1995
Fixes #1979
Fixes #1906
Fixes #2677