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Permissions seem to break when using the subsites module.
Users in groups other than admin can only edit pages on the main site if the 'Edit any page' box is checked, which means you can only allow users to edit all pages or no pages.
If you don't allow them to edit all pages, then every page is in read only mode on the main site.
If you disable the subsite_filter from the _config then it works as expected, but obviously breaks the tree.
Create a Subsite
Create a new Group with a test user in
Give them access to the 'Pages' section
Login with that user and note that no pages on the Main site are editable.
It seems the fix is simple and available here:
Mateusz' fix has been applied, so this issue should be closed