docs: add worked configuration example

[EthemKD]

Closes #5

What does this change?

Adds a complete, commented config.yaml example to docs/configuration.md, based on the repository's current root configuration. The example keeps all existing sections together in one copy-pasteable block and adds concise comments explaining what each section controls.

It also reiterates that NEO4J_USER, NEO4J_PASSWORD, OPENAI_API_KEY, and the optional NEO4J_URI override belong in the environment rather than config.yaml.

Validation

• git diff --check ✅
• uv run ruff check . ✅
• uv run ruff format --check . ✅
• uv run pytest tests/unit: 1177 passed; 1 unrelated local Windows byte-hash provenance test failed (test_quarkus_openapi_provenance.py)

Checklist

• tests added/updated (not needed; documentation-only change)
• documentation updated
• no secrets included
• licensing compatible (no dependencies added)
• backwards compatibility considered

If this adds or changes an adapter

Not applicable.

[michaelegner]

Blocking correctness issue: the worked example is no longer copy-pasteable against current main.

sources.directories now rejects bare strings, so:

directories:
  - examples

fails configuration validation. Each entry must carry stable source identity, for example:

directories:
  - id: aip-bundled-examples-v0.5
    root: examples
    stable_target_identity: urn:aip:logical-root:bundled-examples

Please rebase/update the example to match the current root config.yaml.