A fresh install leaves `permalink_structure` empty, so WordPress snapshots
$wp_rewrite with no post/page permalink rules and every single post resolves
to 404 until someone re-saves Settings -> Permalinks.
The existing mitigation fired too late to help: routing.php wrote the option
and flushed from `init`, but WP_Rewrite was already constructed with the empty
structure, and core defers pre-`wp_loaded` flushes to a `wp_loaded` callback
that regenerates from that stale snapshot. The rewrite_rules option ended up
non-empty but broken, so the 404 persisted on every request.
New \Jio\Core\RewriteBootstrap owns this: on `after_setup_theme` (still inside
wp-settings.php, before wp-blog-header.php parses the query) it calls
$wp_rewrite->set_permalink_structure() — the same API wp-admin/options-permalink.php
uses — which persists the option *and* refreshes the in-memory snapshot, so both
the current request and the rules written for the next one are correct. A
structure an administrator chose is never overridden.
Also consolidates the two duplicated flush sites that lived inline in
functions.php (`after_switch_theme` closure and the `jio_flushed_version`
block, whose `delete_option('rewrite_rules')` forced a needless regenerate),
and drops the now-redundant permalink write from routing.php. The version
stamp moves to `wp_loaded` priority 20 so it sees the complete rule set
instead of the pre-`add_rewrite_rule()` snapshot.
Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>