Harden runtime dependencies, diagnostics paths, and embedding retries

[raitoxlol]

What changed

• Declare PyYAML>=6.0 as a runtime dependency and update uv.lock.
• Resolve diagnostic logs under HERMES_HOME when it is set.
• Retry embedding API HTTP 429/5xx responses and transient network failures with bounded exponential backoff; permanent 4xx errors still fail fast.
• Add regression coverage for the dependency/path/retry behavior and document the fixes in the unreleased changelog.

Why

Clean installs failed during first-run config initialization because the package imported yaml without declaring PyYAML. Diagnostics ignored HERMES_HOME and could write into a different Hermes installation. Transient embedding endpoint failures returned immediately, creating silent embedding gaps.

Validation

• Focused regression tests: 13 passed
• python3 -m compileall: passed
• scripts/verify-docs.py: passed (website docs skipped because the sibling checkout is unavailable)
• python -m build: passed
• Subprocess diagnostic check confirmed logs were written under the configured HERMES_HOME.

The full test suite was not run here; one existing diagnostics test fails because the current implementation closes a database connection that the test later reuses.

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[AxDSan]

Merged in 21ff279. @raitoxlol solid first contribution. Three fixes in one PR, each with focused tests.

• PyYAML dependency declared explicitly
• Diagnostics respect HERMES_HOME
• Embedding API retries with bounded backoff

Fixes #473 and #475. Welcome to the project.