File-level sniffs like WordPress.Files.FileName are evaluated at the file level,
not at code level. They require phpcs:ignore directives to be placed within the
file-level docblock (/** ... */), not in code comments.
Moved all 81 phpcs:ignore pragmas from code comments to the file-level docblocks.
This applies to:
- 79 class files with class-naming convention ignores
- prautoblogger.php with strict-types docblock ignore
- uninstall.php with strict-types docblock ignore
- Added phpcs:ignore for class file naming convention (79 violations)
WordPress.Files.FileName.InvalidClassFileName is a known architectural
issue — class files use short names without prautoblogger- prefix
- Added phpcs:ignore for ->prepare() table interpolation (56 violations)
WordPress.DB.PreparedSQL.InterpolatedNotPrepared: dynamic table names
(prab_generation_logs, prab_cost_logs) require interpolation; ->prepare()
does not support table name placeholders, only column values
- Fixed file-level docblock positioning (2 violations)
prautoblogger.php and uninstall.php: moved declare(strict_types=1) before
file docblock per PHP best practices
Run phpcbf --standard=WordPress-Core across includes/, prautoblogger.php,
and uninstall.php. Fixed 1,362 formatting violations in 75 files:
- Short array syntax: [] → array()
- Line breaking for long function calls
- Consistent indentation
- Function call parameter alignment
No logic changes; purely mechanical formatting.
New Peptide_Linker class scans generated HTML and wraps every mention
of a known peptide in a hyperlink to its /peptides/ database page.
Runs as post-processing in Publisher — no LLM involvement, 100% reliable.
Handles case-insensitive matching, hyphen/space variants, skips existing
<a> tags. Gracefully no-ops if PR Core is not active.
Removed prompt-based peptide linking from Content_Prompts (unreliable).
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
