update-core.php, update.php, and options-general.php no longer work.
index.php, profile.php, plugins.php, upload.php, etc all still seem to work
I have tried deactivating every plugin and reverting my theme to the default, but that didn’t work.
I downloaded a fresh copy of 4.9.2, and used my current wp-config.php with it, but the pages still did not work.
I can activate and deactivate plugins, change the appearance of pages and content, but I cannot update or delete any plugins.
WP_DEBUG and WP_DEBUG_LOG didn’t reveal anything.
What steps can I take to troubleshoot this? Is something in the SQL database corrupted?
https://core.trac.wordpress.org/ticket/42345
After a lot of digging and following segfaults in strace and parsing out apache core dumps (and enlisting some outside help from a much more knowledgeable Linux guy) I dug this up on WordPress’s site.
The short answer to the problem is that there is an issue with PHP5 and libssh2 that was introduced in an update a few months ago. There is no actual fix for it, but it can be effectively worked around by installing this plugin: https://wordpress.org/plugins/ssh-sftp-updater-support/
It worked like a charm for me; all my users can log in normally and I can once again update plugins and WP Core through the GUI.
Hope this works for you, and others!
