Fix 12 spec inconsistencies from SDK testing report

Generation script fixes (fix_spec_issues):
- Generate operationId for all 52 platform endpoints
- Remove phantom /v2/sandboxes/{sandboxID}/logs deprecation reference
- Complete truncated 'start'/'end' parameter descriptions on metrics
- Fix sandboxId → sandboxID casing in 502 error schema
- Add security: [] and 'health' tag to GET /health
- Remove YAML anchor overlay on /files responses (DownloadSuccess/UploadSuccess)
- Add type: object to 53 schemas missing it
- Move 'end' param description out of schema to sibling level

Also fix fill_empty_responses to skip $ref responses.

Upstream issues not fixable in spec:
- allow_internet_access snake_case (server field name)
- Duplicate EntryInfo schemas (different APIs)
- Inconsistent error response coverage (API behavior)
- Auth inconsistency across template versions (intentional v1→v2/v3)

Author: beran-t