- Add abbrs field to Established verdict taxonomy item
- Add peptide_starter_render_desc() helper — builds safe HTML from
esc_html/esc_attr components; replaces abbr terms with <abbr> tap-targets
- Update front-page.php description output to use render_desc()
- Add assets/js/abbr-tooltip.js — popover open/close, outside-click
dismissal, keyboard accessibility (Enter/Space/Escape), ARIA attrs
- Enqueue abbr-tooltip.js on is_front_page() only
- Add .pr-abbr and .pr-abbr-popover CSS with dashed underline affordance,
fade-in animation, dark-mode-safe surface variables
- Fix PEPTIDE_STARTER_VERSION drift: 2.0.0-alpha.3 → 2.2.1
Routing note: this is a theme change (not PR Core). Term 'RCT' is scoped
to the verdict legend strip only; monograph bodies are unaffected.
Security-only release per ADR-0001. Closes all six ship-blockers from the
post-v1.5.0 audit: PSEC-001 (no rate limiting), PSEC-002 (account
enumeration via separate error messages), PSEC-003 (registration auto-login
with no email verification), PSEC-004 (ungated "My Data" templates),
PSEC-005 (CSV formula injection on subscriber export), PSEC-006 (no
honeypot/CAPTCHA on public forms).
Adds inc/config.php (single source of truth for all security thresholds,
filterable via peptide_starter_security_config), inc/rate-limiter.php
(Peptide_Starter_Rate_Limiter + Cloudflare-aware client IP resolver,
transient-backed, never stores raw IPs), and inc/email-verification.php
(43-char token, 24h TTL, /verify rewrite, rate-limited resend endpoint).
Auth handlers rewritten to: unify all failure messages, rate-limit before
any expensive check, drop registrations with a filled honeypot silently,
stop auto-login on register, send a verification email instead. The
require_login() helper lives in inc/helpers.php and is applied at the top
of page-tracker.php, page-subject-log.php, and page-protocol-builder.php;
page-calculator.php stays open (no PII, no writes).
Newsletter signup gains: consent checkbox, privacy link, honeypot,
autoload=false on the wp_options blob, unsubscribe token stored per row,
/newsletter-unsubscribe route, merged success+duplicate into a single "ok"
state. Admin export runs every cell through peptide_starter_csv_safe()
which prefixes leading =/+/-/@/tab/CR with a quote.
Contact handler hardens against email-header injection (rejects name
values with \r \n , < >), rate-limits, honors honeypot, tags mail
failures with a request ID for correlation without logging message
content.
Adds Tools → Mail Test (inc/mail-diagnostic.php): a permanent wp_mail
probe so we can check Hostinger outbound deliverability any time it looks
flaky. Adds a one-time admin_init migration that enrols pre-v1.5.1
subscribers into the verification flow (currently a no-op — zero users —
but guarded for the future).
Other cleanup from the audit: fallback primary menu moved out of
header.php into inc/helpers.php (redeclaration risk), placeholder footer
language links replaced with "Translations coming soon", footer copyright
now reads through the customizer getter, settings-panel gains a proper
Tab/Shift+Tab focus trap and saves/restores body overflow, documentation
heading IDs slugified from heading text with collision counters, JS files
standardized on const/let.
Six new PHPUnit suites cover rate limiter lifecycle, auth handler error
unification and rate limits, email verification token generation and
expiry, contact handler header injection + rate limit + honeypot,
newsletter signup consent + CSV safety, and require_login gate behavior.
ARCHITECTURE.md and CONVENTIONS.md updated in the same commit — new
module layout, data flows, security patterns for rate-limiting,
honeypotting, gating, and CSV-safe export.
Version bumped to 1.5.1 in style.css and functions.php.
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Major theme extension adding full-featured navigation with dropdown submenus (Tools, My Data, Resources),
9 new page templates (Calculator, Protocol Builder, Tracker, Subject Log, Documentation, Directory,
Science Feed, Profile, Sign In/Register), documentation page with sidebar ToC and scroll spy,
branded AJAX authentication forms, newsletter signup with admin export, slide-out contact/support panel,
Research Modules 6-card grid on front page, and comprehensive footer update.
Split functions.php (554→206 lines) into 6 focused inc/ modules: helpers, customizer, auth-handlers,
contact-handler, page-setup, newsletter-admin. All new components include dark mode support, CSRF
protection, input sanitization, output escaping, and graceful plugin degradation via shortcode_exists().
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
- Convert all PHP files from CRLF to LF line endings
- Reformat multi-line function calls per WPCS standard
(opening paren last on line, closing paren on own line)
- Fix assignment-in-conditional in single-peptide.php
- Change double quotes to single quotes in content-none.php
- Exclude InvalidClassFileName sniff (standard WP functions.php pattern)
- Fix archive-peptide.php opening PHP tag placement
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
