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feat: initial peptide-repo-core plugin (v0.1.0) — canonical schema sprint

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Implements ADR-0002: canonical peptide schema as shared data layer for
the peptiderepo.com ecosystem. All Tier 1 tools (Reconstitution Calculator,
Dosage Reference, Legal Status Tracker, PSA enhancements) build on this.

Includes:
- pr_peptide CPT with REST, taxonomies, 11 meta fields
- 3 custom tables: pr_dosing_rows, pr_legal_cells, pr_ai_candidate_queue
- Sequential migration runner with schema versioning
- 4 typed DTOs and 4 repository classes (full CRUD)
- REST API (pr-core/v1): 6 endpoints (read public, write auth-gated)
- Admin UI: 3 meta boxes, custom columns, AI candidate queue page
- Shared disclaimer component (shortcode + static API)
- JSON-LD Drug schema emission on single peptide pages
- Seed data fixture (3 peptides, 10 dosing rows, 5 legal cells)
- Full teardown in uninstall.php
- CI: PHP lint 8.0-8.2, PHPCS WordPress, 300-line check

All 22 PHP files under 300 lines. Highest: peptide-cpt at 265.

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
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peptiderepo
2026-04-17 07:36:12 +07:00
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# Peptide Repo Core — Conventions
## Naming
- **Class prefix:** `PR_Core_` — all classes use this prefix.
- **Hook prefix:** `pr_core_` — all actions and filters start with this.
- **Option prefix:** `pr_core_` — all wp_options keys start with this.
- **Table prefix:** `pr_` — custom tables use `{wpdb->prefix}pr_*`.
- **CSS prefix:** `.pr-core-` — admin and frontend styles.
- **Text domain:** `peptide-repo-core`.
## File Naming
Autoloader convention: `PR_Core_Foo_Bar` maps to `class-pr-core-foo-bar.php`.
Files live in `includes/` or one level of subdirectory under `includes/`.
## How To: Add a New Post-Meta Field
1. Add the field to `PR_Core_Peptide_CPT::get_meta_fields()` in `cpt/class-pr-core-peptide-cpt.php`.
2. Add the field to `PR_Core_Peptide_DTO` constructor and `to_array()` in `dto/class-pr-core-peptide-dto.php`.
3. Add the field to `PR_Core_Peptide_Repository::post_to_dto()` in `repositories/class-pr-core-peptide-repository.php`.
4. Add a form input in `PR_Core_Peptide_Metaboxes::render_identifiers_box()` in `admin/class-pr-core-peptide-metaboxes.php`.
5. The `save_meta()` method reads from the same field list — no changes needed unless custom save logic applies.
## How To: Add a New Migration
1. Create `includes/migrations/class-pr-core-migration-NNNN-description.php`.
2. The class must be named `PR_Core_Migration_NNNN_Description` with a public `up()` method.
3. Add the class name to `PR_Core_Migration_Runner::MIGRATIONS` array (index = version - 1).
4. Bump `PR_CORE_TARGET_SCHEMA_VERSION` in `peptide-repo-core.php`.
5. All migrations must be idempotent (safe to run twice).
## How To: Add a New REST Endpoint
1. Add a `register_rest_route()` call in `PR_Core_Rest_Controller::register_routes()`.
2. Implement the callback method in the same class.
3. Use `check_write_permission()` for any write endpoints.
4. Return typed DTOs via `->to_array()` for consistent response shape.
## How To: Add a New Disclaimer Surface
1. Add a default text entry in `PR_Core_Disclaimer::DEFAULTS`.
2. Use `[pr_disclaimer surface="new-surface"]` in templates.
3. Custom copy can be set via `PR_Core_Disclaimer::update_disclaimer()`.
## Error Handling
- Repository methods return `null` or `0` on failure, never throw.
- REST endpoints return `WP_Error` with appropriate HTTP status codes.
- All database queries use `$wpdb->prepare()` for parameterization.
- Admin actions verify nonces and capabilities before processing.
## Evidence Strength Enum
Ordered weakest to strongest: `preclinical`, `case-series`, `observational`, `rct-small`, `rct-large`, `meta-analysis`. Validated by `PR_Core_Peptide_CPT::sanitize_evidence_strength()`.
## Legal Status Enum
Values: `prescription`, `ruo`, `otc`, `restricted`, `banned`, `unclear`. Validated by `PR_Core_Legal_Repository::sanitize_row()`.
## Supersede Pattern (Soft Delete)
Dosing rows and legal cells use a `superseded_by_id` column instead of hard deletes. When a correction is needed, the old row gets `superseded_by_id` set to the new row's ID. Queries for "active" data filter on `superseded_by_id IS NULL`. This preserves full audit history.