fix(bundle-loader): preserve root instruction with AGENTS context

[Brian Krabach (bkrabach)]

Summary

• Preserve the root instruction while appending the CLI's optional home and project .amplifier/AGENTS.md mentions.
• Add regression coverage for behavior composition, fresh per-request resolution, resume, and cached-bundle reuse.

Why/design

• Appending the tail after behavior composition preserves the prompt and bodyless-inheritance behavior.
• A shallow copy avoids cache accumulation when the same registry is reused.
• The normal resolver handles optional files and refreshes them per request; no plain cwd/AGENTS.md is added by the CLI.

Tests

• uv run --with truststore==0.10.4 pytest -q — 2083 passed, 1 skipped, 13 deselected, 1 xfailed.
• uv run --with truststore==0.10.4 pytest -q tests/lib/bundle_loader/test_root_instruction_survives_behaviors.py — 11 passed.
• DTU 23/23 provider-bound assertions across real fresh/run --resume, custom vs. actual anchors context.
• Deterministic provider and minimal context/orchestrator plus persistence-hook coverage; partial-bundle mode excludes unrelated app-behaviors.
• No live vendor tested; this does not claim a full default-stack run.

Compatibility/scope

• CLI-only change using the existing API; no foundation edits, workspace commits, version bump, merge, or auto-merge.
• No breaking changes; missing optional files remain non-fatal and are resolved dynamically per request.