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peptiderepo 850279e756 feat(cpt): consolidate peptide CPT with PSA; drop pr_peptide (v0.2.0)

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

2026-04-22 08:32:00 +00:00

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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

Add the field to PR_Core_Peptide_CPT::get_meta_fields() in cpt/class-pr-core-peptide-cpt.php.
Add the field to PR_Core_Peptide_DTO constructor and to_array() in dto/class-pr-core-peptide-dto.php.
Add the field to PR_Core_Peptide_Repository::post_to_dto() in repositories/class-pr-core-peptide-repository.php.
Add a form input in PR_Core_Peptide_Metaboxes::render_identifiers_box() in admin/class-pr-core-peptide-metaboxes.php.
The save_meta() method reads from the same field list — no changes needed unless custom save logic applies.

How To: Add a New Migration

Create includes/migrations/class-pr-core-migration-NNNN-description.php.
The class must be named PR_Core_Migration_NNNN_Description with a public up() method.
Add the class name to PR_Core_Migration_Runner::MIGRATIONS array (index = version - 1).
Bump PR_CORE_TARGET_SCHEMA_VERSION in peptide-repo-core.php.
All migrations must be idempotent (safe to run twice).

How To: Add a New REST Endpoint

Add a register_rest_route() call in PR_Core_Rest_Controller::register_routes().
Implement the callback method in the same class.
Use check_write_permission() for any write endpoints.
Return typed DTOs via ->to_array() for consistent response shape.

How To: Add a New Disclaimer Surface

Add a default text entry in PR_Core_Disclaimer::DEFAULTS.
Use [pr_disclaimer surface="new-surface"] in templates.
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.

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