850279e756
Resolves the rewrite slug collision that was 404'ing all 89 production peptide detail pages. PR Core v0.1.1 registered an empty pr_peptide CPT claiming /peptides/%postname%/; WP's rewrite resolver picked it over PSA's populated peptide CPT. This release consolidates both registrations onto a single peptide CPT owned by PR Core. PSA v4.5.0 drops its registration in favor of this one. ## Contract (per CTO msg 02) - POST_TYPE: pr_peptide -> peptide - TAX_CATEGORY: pr_peptide_category -> peptide_category - TAX_FAMILY const removed (pr_peptide_family was never populated) - CPT + taxonomy registration guarded with post_type_exists() / taxonomy_exists() so deploy order between PR Core and PSA is forgiving - Args harmonized as superset of PSA + prior PR Core (thumbnail added to supports; capability_type + map_meta_cap preserved) - Activator: flush_rewrite_rules(false) on activation; new maybe_flush_on_version_change() handler hooked at init:999 for in-place updates that bypass the activation hook (e.g. SCP deploys) - uninstall.php: blanket DELETE replaced with JOIN on _pr_core_authored so PSA-authored peptide posts (the 89 canonical monographs) are never destroyed; peptide_category terms preserved (shared ownership) - Scrub scope: narrow — CPT-slug-derived identifiers only; class names, file names, PR_CORE_* constants, pr_core_* options, and pr-core/v1 REST namespace remain ## Docs - ARCHITECTURE.md: new Key Decision #7 (v0.2.0 consolidation) and §2.9 Uninstall specification - CONVENTIONS.md: CPT Ownership rule + _pr_core_authored flag contract ## Tests - Lightweight harness (tests/bootstrap.php) that stubs the handful of WP functions exercised by the CPT class - tests/unit/test-peptide-cpt.php asserts: constants match contract, TAX_FAMILY is removed, guard no-ops when post_type_exists/taxonomy_exists returns true, args payload shape (thumbnail in supports, rewrite slug, REST namespace), hooks wired - CI: new 'Unit tests (lightweight, no PHPUnit)' step in lint-php job, runs across PHP 8.1/8.2/8.3. Full PHPUnit + wp-env harness is a follow-up Refs: convo/prcore/threads/2026-04-peptides-cpt-collision/02-cto-correction.md
199 lines
12 KiB
Markdown
199 lines
12 KiB
Markdown
# Peptide Repo Core — Architecture
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Peptide Repo Core is a WordPress plugin that provides the canonical peptide data layer for the peptiderepo.com ecosystem. It owns the `peptide` custom post type (consolidated in v0.2.0; previously registered by Peptide Search AI pre-schema-sprint — PSA v4.5.0 drops its registration in favor of this one), the `peptide_category` taxonomy, custom tables for dosing rows and legal status cells, typed repository classes, an AI candidate queue for semi-automated data extraction, a shared disclaimer component, and JSON-LD structured data output. Every consumer plugin (PR Theme, PRAutoBlogger, Peptide News, Peptide Search AI, and all Tier 1 tools) reads peptide data through this plugin's versioned PHP API, never directly.
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**Ownership model (v0.2.0+).** PR Core is the sole registrant of the `peptide` CPT and `peptide_category` taxonomy. Registration is guarded by `post_type_exists()` / `taxonomy_exists()` so a second registration from any other plugin (historically PSA, which now defers) no-ops cleanly and deploy order between plugins does not matter. See CONVENTIONS.md for the CPT ownership rule.
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---
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## Data Flow
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```
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┌───────────────────────┐
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│ PubMed / Literature │
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└──────────┬────────────┘
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│ (future: extraction pipeline)
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▼
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┌───────────────────────┐
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│ AI Candidate Queue │ pr_ai_candidate_queue table
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│ (pending → review) │ Confidence-sorted
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└──────────┬────────────┘
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│ Approve
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▼
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┌──────────────────┐ ┌───────────────────────┐ ┌──────────────────┐
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│ Admin UI / REST │───▶│ Dosing Repository │───▶│ pr_dosing_rows │
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│ (manual entry) │ │ Legal Repository │ │ pr_legal_cells │
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└──────────────────┘ └───────────────────────┘ └──────────────────┘
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│
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▼
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┌───────────────────────┐
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│ Peptide Repository │ peptide CPT + meta
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└──────────┬────────────┘
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│
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┌───────────────┼───────────────┐
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▼ ▼ ▼
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┌──────────┐ ┌──────────┐ ┌──────────┐
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│ REST API │ │ JSON-LD │ │ Consumer │
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│ pr-core │ │ Drug │ │ Plugins │
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│ /v1/ │ │ schema │ │ via API │
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└──────────┘ └──────────┘ └──────────┘
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```
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---
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## File Tree
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```
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peptide-repo-core/
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├── peptide-repo-core.php # Plugin bootstrap — constants, autoloader, activation hooks
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├── uninstall.php # Selective teardown: plugin-owned posts + tables + options + caps
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├── ARCHITECTURE.md # This file
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├── CONVENTIONS.md # Naming patterns, extension guides
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├── CHANGELOG.md # Semantic versioning changelog
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├── composer.json # Dev dependencies (PHPCS, WPCS) and lint scripts
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├── phpcs.xml.dist # PHPCS ruleset configuration
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│
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├── .github/
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│ └── workflows/
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│ └── ci.yml # PHP lint (8.1-8.3), PHPCS WordPress, 300-line check, unit tests
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│
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├── assets/
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│ └── css/
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│ └── admin.css # Minimal admin meta box styles
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│
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├── includes/
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│ ├── class-pr-core.php # Main orchestrator — boots subsystems, registers public filters
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│ ├── class-pr-core-activator.php # Activation + version-change flush handler
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│ ├── class-pr-core-deactivator.php # Deactivation: rewrite flush only (data preserved)
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│ ├── class-pr-core-autoloader.php # SPL autoloader for PR_Core_ prefixed classes
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│ ├── class-pr-core-seed-data.php # Dev fixture: 3 peptides, 10 dosing rows, 5 legal cells
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│ │
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│ ├── cpt/
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│ │ └── class-pr-core-peptide-cpt.php # CPT + peptide_category registration (guarded), meta fields, sanitizers
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│ │
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│ ├── migrations/
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│ │ ├── class-pr-core-migration-runner.php # Sequential migration engine
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│ │ ├── class-pr-core-migration-0001-dosing-rows.php # pr_dosing_rows table
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│ │ ├── class-pr-core-migration-0002-legal-cells.php # pr_legal_cells table + unique constraint
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│ │ └── class-pr-core-migration-0003-candidate-queue.php # pr_ai_candidate_queue table
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│ │
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│ ├── dto/
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│ │ ├── class-pr-core-peptide-dto.php # Typed peptide value object
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│ │ ├── class-pr-core-dosing-row-dto.php # Typed dosing row value object
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│ │ ├── class-pr-core-legal-cell-dto.php # Typed legal cell value object
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│ │ └── class-pr-core-candidate-dto.php # Typed candidate queue value object
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│ │
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│ ├── repositories/
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│ │ ├── class-pr-core-peptide-repository.php # CRUD for peptide CPT
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│ │ ├── class-pr-core-dosing-repository.php # CRUD for pr_dosing_rows
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│ │ ├── class-pr-core-legal-repository.php # CRUD for pr_legal_cells
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│ │ └── class-pr-core-candidate-queue-repository.php # CRUD + approve/reject for queue
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│ │
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│ ├── admin/
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│ │ ├── class-pr-core-admin.php # Admin initialization, menu, styles
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│ │ ├── class-pr-core-peptide-metaboxes.php # Identifiers, dosing, legal meta boxes
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│ │ ├── class-pr-core-admin-columns.php # Evidence, editorial, dosing count columns
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│ │ └── class-pr-core-candidate-queue-page.php # AI candidate review admin screen
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│ │
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│ ├── frontend/
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│ │ ├── class-pr-core-disclaimer.php # Shortcode + static API for surface disclaimers
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│ │ └── class-pr-core-jsonld.php # schema.org Drug JSON-LD on single peptide pages
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│ │
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│ └── api/
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│ └── class-pr-core-rest-controller.php # REST endpoints for peptides, dosing, legal
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│
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└── tests/
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├── bootstrap.php # Lightweight WP function mocks for no-PHPUnit unit runs
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└── unit/
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└── test-peptide-cpt.php # CPT + taxonomy guard + args payload assertions
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```
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---
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## Custom Tables
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### `{prefix}pr_dosing_rows`
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High-cardinality dosing data, 1:many with peptide. Indexed on peptide_id, route, population, pubmed_id.
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Supersede pattern: corrections create a new row and set `superseded_by_id` on the old one.
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### `{prefix}pr_legal_cells`
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Per-country legal status, 1:many with peptide. Unique constraint on (peptide_id, country_code, superseded_by_id) — only one active cell per peptide x country.
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### `{prefix}pr_ai_candidate_queue`
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AI-extracted dosing candidates. Status flow: pending → approved/rejected → merged (if approved). Approved rows copy into `pr_dosing_rows` with `source = 'ai-candidate-approved'`.
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---
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## Public API
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### Repositories (typed DTOs, never raw objects)
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- `PR_Core_Peptide_Repository` — find_by_id, find_by_slug, search, find_all, count
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- `PR_Core_Dosing_Repository` — find_by_id, find_by_peptide, insert, supersede, count_by_peptide
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- `PR_Core_Legal_Repository` — find_by_id, find_by_peptide, find_by_peptide_and_country, find_by_country, insert, supersede
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- `PR_Core_Candidate_Queue_Repository` — find_by_id, find_by_status, insert, approve, reject, count_by_status
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### Filters
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- `pr_core_get_indexable_corpus` — returns `{ id, url, title, body, type }` entries for search indexing
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- `pr_core_disclaimer_for_surface` — returns disclaimer text for a given surface identifier
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- `pr_core_evidence_strength_label` — maps enum value to localized label
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- `pr_core_jsonld_peptide` — filter JSON-LD schema before output
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- `pr_core_register_peptide_fields` — add computed fields to peptide DTO (planned)
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### Actions
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- `pr_core_before_peptide_publish`, `pr_core_after_peptide_publish`
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- `pr_core_before_dosing_row_publish`, `pr_core_after_dosing_row_publish`
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- `pr_core_before_legal_cell_publish`, `pr_core_after_legal_cell_publish`
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- `pr_core_candidate_approved`, `pr_core_candidate_rejected`
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### REST API (namespace: `pr-core/v1`)
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| Method | Endpoint | Auth | Description |
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|--------|----------|------|-------------|
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| GET | /peptides | Public | List peptides with filters |
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| GET | /peptides/{id} | Public | Single peptide |
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| GET | /peptides/{id}/dosing | Public | Dosing rows for peptide |
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| POST | /peptides/{id}/dosing | manage_peptide_content | Add dosing row |
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| GET | /peptides/{id}/legal | Public | Legal cells for peptide |
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| POST | /peptides/{id}/legal | manage_peptide_content | Add legal cell |
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---
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## Key Decisions
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### #1: Separate plugin for canonical schema
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Consumer plugins read through versioned PHP API + hooks, never direct table access. Decouples domain schema from feature lifecycle. See ADR-0002.
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### #2: Custom tables for dosing and legal data
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Post-meta doesn't scale for high-cardinality data queried by multiple dimensions (peptide + route + population). Custom tables with proper indexes.
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### #3: Supersede pattern instead of hard deletes
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Corrections create new rows; old rows get `superseded_by_id`. Preserves full audit trail for regulatory accountability.
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### #4: AI candidate queue with human-in-the-loop
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Automated extraction populates the queue; humans approve/reject. Approved rows copy into dosing table with provenance tracking (`source`, `ai_candidate_id`).
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### #5: Disclaimer component owned by core
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Single editorial review point. All consumer plugins render the same versioned disclaimer text. Surface-specific copy (dosing, legal, reconstitution, AI answer) stored in one wp_option.
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### #6: JSON-LD from day one
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Drug schema on single pages increases LLM citation rate. Filter hook allows consumer plugins to extend the schema object.
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### #7: PR Core owns the `peptide` CPT and `peptide_category` taxonomy (v0.2.0)
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Prior to v0.2.0, PR Core registered `pr_peptide` while Peptide Search AI registered `peptide` — both claimed the public rewrite slug `peptides`, and WP's rewrite resolver picked PR Core's empty CPT, 404'ing all 89 production peptide detail pages. v0.2.0 consolidates both registrations onto a single `peptide` CPT, owned by PR Core. PSA v4.5.0 drops its CPT/taxonomy registration; its meta boxes (`psa_peptide_data`, `psa_extended_data`), directory shortcode, KB article renderer, and search widget continue operating on the shared `peptide` CPT regardless of who registers it. Registration on both sides is guarded with `post_type_exists()` / `taxonomy_exists()` so deploy order is forgiving.
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## §2.9 Uninstall specification
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PR Core `uninstall.php` removes plugin-owned data only:
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1. **Drops custom tables** — `pr_dosing_rows`, `pr_legal_cells`, `pr_ai_candidate_queue`.
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2. **Deletes `peptide` posts only if they carry the `_pr_core_authored` meta flag.** The 89 canonical peptide posts predate PR Core and were authored via PSA; they are never blanket-deleted on PR Core uninstall.
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3. **Does not delete `peptide_category` terms.** Shared-ownership taxonomy; term metadata the site relies on outlasts this plugin.
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4. **Deletes `pr_core_*` options.**
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5. **Removes `manage_peptide_content` capability from all roles.**
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