feat: support empty-project initialization from references and emit reference metadata

[clawdeeo]

Wires the reference pipeline into an end-to-end initialization flow and adds deterministic reference metadata rendering.

Changes

• scripts/lib/reference_initialization.py:
  • is_empty_target() — detects empty/near-empty targets (zero files, no tree, no config/git/tests)
  • build_reference_metadata() — builds ReferenceMetadata from loaded documents, preserves order, includes commit SHA
  • render_reference_metadata_block() — renders metadata as Markdown HTML comment with JSON body
  • ReferenceInitializationResult — structured result with adapted_references, questions, metadata, warnings
  • initialize_from_references() — end-to-end: detect empty, adapt, generate questions, build metadata
  • successful_reference_documents() — extracts successful documents from ReferenceLoadResult list
  • AGENTSKILL_VERSION = "0.5.0"
• 20 tests covering empty/non-empty detection, metadata serialization, block rendering with JSON roundtrip, order preservation, warnings, version

Not included

• CLI flags or interactive prompts
• Direct file writing
• Reference loader changes
• Synthesis redesign

177 tests pass. ruff + mypy clean.