feat(run): preserve sourced harness config

[slowdini]

Closes #260
Part of #244

Why

Realistic codebase-backed evals inherit the repository's agent instructions, harness settings, and
project skills. Preserving that configuration is important for fidelity, but a checked-in copy of
the subject or a staged sibling can contaminate both sides of the comparison. Operator-installed
skills and codebase-provided skills also need different remedies, so treating both as one shadow
source obscures what the evaluator should do.

Strategy

• Treat the harness descriptor as the source of truth for project skill discovery. skills_dir
  remains the only staging destination, while additional_project_skill_dirs declares
  cross-harness compatibility roots such as OpenCode's .claude/skills and .agents/skills.
• Inventory matching project skills immediately after codebase provisioning, before exclusion or
  staging can replace them. Preserve all codebase config by default and emit distinct
  codebase-sourced findings in schema-v3 plugin-shadow.json.
• Add the per-eval codebase.exclude_skill_sources escape hatch. It moves every declared project
  skill root aside symmetrically in both comparison arms, including revision mode and --no-stage,
  while leaving CLAUDE.md, AGENTS.md, settings, and plugins in place.
• Reuse the staging manifest's backup/restore model for generated-slug collisions and excluded
  roots. Generated staging names displace and restore an occupied directory; explicit
  --stage-name values still refuse to clobber one.
• Keep operator isolation and codebase policy independent. A descriptor's
  isolates_live_sources = true assertion suppresses only operator-environment findings;
  preserved codebase findings remain validity warnings.
• Carry the effective exclusion value through conditions.json, dispatch.json, every
  run.json, benchmark.json, and promoted BASELINE.md provenance.

Safety and compatibility boundaries

• The default remains preservation: project instructions and harness configuration are never
  broadly stripped from sourced codebases.
• Exclusion is descriptor-scoped and symmetric. A rootless BYOH descriptor records the policy but
  performs no filesystem mutation.
• Cleanup validates that restored roots belong to the resolved descriptor and that backups live in
  runner-managed temporary directories before removing the active skills directory.
• Readers accept schema-v2 and historical unversioned shadow artifacts; writers emit schema v3
  with an explicit finding class.

Configuration example

{
  "codebase": {
    "url": "https://github.com/slowdini/example-project",
    "ref": "v1.4.0",
    "exclude_skill_sources": true
  }
}

For OpenCode, this excludes .opencode/skills, .claude/skills, and .agents/skills because its
descriptor declares all three roots. Other project configuration remains available to the agent.

Verification

• cargo fmt --check
• cargo build
• cargo test — 911 library tests, 184 CLI tests, 182 run tests, and doc tests
• cargo clippy --all-targets -- -D warnings
• git diff --check