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>
Reformat add_setting() and add_control() calls to comply with
PEAR.Functions.FunctionCallSignature — each argument on its own line,
opening paren last on line, closing paren on its own line. Matches the
pattern already used by add_section() calls in the same file.
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>
Reduce hero padding from 96/80px to 64/48px, shrink subtitle and
search margins, tighten news-feed and archive section padding,
and reduce peptides grid gap for better content density.
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Warm off-white light palette, decorative geometric shapes,
category-coded peptide cards with tinted borders and pill badges,
larger hero typography with accent word, header CTA button,
and redesigned single-peptide detail page with meta card grid.
Dark mode stays default per user preference. Light mode gets the
warm treatment when toggled or via prefers-color-scheme.
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
The CI was overriding the project PHPCS config by passing
--standard=WordPress-Core directly. Now uses the project
.phpcs.xml.dist which includes exclusions for standard WP
patterns (class in functions.php).
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>
Wrapped get_search_query() with esc_attr() in 404.php, front-page.php,
and searchform.php. Without this, a crafted search query can inject
arbitrary HTML attributes into the search input value field.
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Renders PRAutoBlogger-generated research articles as a card grid
between the hero section and the peptide news feed. Wrapped in
shortcode_exists() so it degrades gracefully if the plugin is
deactivated.
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
