docs+fix: update documentation and API responses for post-0.3.0 changes

[bburda]

Summary

Documentation and API responses are out of sync with code after logging endpoints, merge pipeline, and plugin system changes landed on main.

Broken for users (docs):

• tutorials/manifest-discovery.rst documents config.unmanifested_nodes with 4 policies (ignore/warn/error/include_as_orphan) - this parameter does not exist. Replaced by discovery.merge_pipeline.gap_fill.*.

Missing documentation:

• config/server.rst missing Logging (logs.buffer_size) and Rate Limiting (rate_limiting.*) config sections
• config/discovery-options.rst missing entire merge pipeline section (gap_fill, layer policies, field groups)
• tutorials/plugin-system.rst marks IntrospectionProvider as "preview/not yet wired" (now wired via PluginLayer) and is missing LogProvider
• api/rest.rst server capabilities example response wrong format and outdated

Code bugs (handle_root / version-info):

• GET /api/v1/ missing entire endpoint categories: logs, bulk-data, cyclic-subscriptions, updates
• GET /api/v1/ capabilities JSON missing: logs, bulk_data, cyclic_subscriptions, updates
• GET /api/v1/ lists ghost snapshot endpoints with no registered routes
• Version hardcoded as "0.1.0" in handle_root and version-info (should be 0.3.0)
• GET /version-info uses sovd_info key instead of SOVD-standard items
• Entity capability responses missing bulk-data, logs, cyclic-subscriptions URIs

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Proposed solution

Update docs, fix handle_root/version-info responses, add missing entity capability URIs, update tests.

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Additional context

Changes landed between 0.3.0 (Feb 27) and current main: logging endpoints (#245), merge pipeline, plugin system IntrospectionProvider wiring, LogProvider interface.