Additive: iterative editor↔writer loop bounded by editorial_max_rounds (default 3), escalates to Review Queue on exhaustion, records each round; behind interface, Authority-only (live path untouched). Also deletes dead class-research-dedup.php + repairs ARCHITECTURE.md. QA APPROVE 16035fa; CI green (VPS-verified).
Agent-Session: prab-phase2b-2-merge
Pipeline v2 Phase 1, commit 2/4. Prompt_Registry (read) +
Prompt_Registry_Writer (immutable create/activate/seed) over the new
prompts table; canonical v1 bodies extracted verbatim into
Prompt_Defaults(+Editorial) — single source for BOTH the seed migration
(Migrate_Prompt_Seed_V0180, flag-gated, self-healing) and the in-code
fallback, so a missing table renders byte-identical prompts and never
fatals. Call sites swapped: Content_Prompts, Analysis_Prompts,
Chief_Editor, LLM_Research_Provider. Includes the image-composer seam
keys image.rewriter_system + image.style_template (composer PR consumes,
must not add its own prompt storage).
Pinning: Cost_Tracker::set_run_id() registers the process run context,
ensures the runs ledger row, and pins active versions once per run;
log_api_call/log_image_generation stamp prompt_version (run pins) +
agent_role (stage map) on every generation_log row. Single-pass keeps
stage 'draft' and stamps content.single_pass explicitly.
Under-300 refactors: Content_Generator's four duplicated span/log blocks
consolidated into execute_stage() (301 -> 224 lines, behavior
identical); get_avg_tokens_for_stages body moved to Cost_Reporter with a
delegating wrapper kept for API compatibility.
Tests: byte-identical fallback renders (single_pass/outline/polish/
editor.system), token filling, key coverage incl. stage-map integrity.
Agent-Session: pipeline-v2-phase1-engineer-20260612
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>
When any peptide from the PR Core database is mentioned in a generated
article, the first mention is now automatically linked to its /peptides/
page. Gracefully degrades if PR Core is not active.
Extracted all prompt construction into Content_Prompts (252 lines),
slimming Content_Generator from 324 → 162 lines. Both under 300.
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
