# 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.

## CPT Ownership

- **One plugin owns each CPT.** PR Core owns the `peptide` CPT and the `peptide_category` taxonomy (as of v0.2.0). No other plugin in this ecosystem registers these post types or taxonomies directly.
- **All registrations must guard with existence checks.** CPT registrations call `if ( post_type_exists( $slug ) ) return;` before `register_post_type()`, and taxonomy registrations call `if ( taxonomy_exists( $slug ) ) return;` before `register_taxonomy()`. This makes deploy order between plugins irrelevant — whichever runs first wins, the other no-ops — and prevents rewrite-slug collisions when two plugins temporarily overlap during a transition.
- **Consumers read, do not register.** Plugins that need to query or display `peptide` posts (PSA, PR Theme, PRAutoBlogger, Peptide News, Tier 1 tools) call `get_posts( [ 'post_type' => 'peptide' ] )` / `WP_Query` without registering the CPT themselves. If a consumer plugin needs its own custom post type for a different domain (e.g., `reconstitution_protocol`), it registers its own slug and does not touch `peptide`.
- **Meta keys are plugin-namespaced, not CPT-namespaced.** PR Core writes `_pr_core_*` or bare keys registered via `register_post_meta()`. PSA writes `psa_*`. The two namespaces coexist on the same `peptide` post because they don't collide.

## `_pr_core_authored` Flag

Any `peptide` post created via PR Core's own UI (not authored via PSA's meta boxes) must be tagged with post-meta key `_pr_core_authored` = `1`. This is the flag `uninstall.php` uses to scope teardown to plugin-owned posts only. Posts originating from PSA (the 89 canonical peptide monographs on production) do not carry this flag and are never deleted on PR Core uninstall.