Security fixes for 10.1 RC

See merge request gitlab/gitlabhq!2209

Adds a test for flattenedFiles
Changes the data method to not be an arrow method
Various other review fixes

This moves away from storing in a single array just to render the table.
It now stores in a multi-dimensional array/object type where each entry
in the array can have its own tree. This makes storing the data for
future feature a little easier as there is only one way to store the
data.

Previously to insert a directory the code had to insert the directory
& then the file at the right point in the array. Now the directory
can be inserted anywhere & then a file can be quickly added into this
directory.

The rendering is still done with a single array, but this is handled
through underscore. Underscore takes the array & then goes through
each item to flatten it into one. It is done this way to save changing
the markup away from table, keeping it as a table keeps it semantically
correct.

Rename classes to (hopefully) clearer names while we're doing that.

This prepares the codebase for a Gitaly migration. See
https://gitlab.com/gitlab-org/gitaly/issues/553

And several other failures

Not all_groups, since that would expose groups the user does not have
access to

In GitLab EE, a GitLab instance can be read-only (e.g. when it's a Geo
secondary node). But in GitLab CE it also might be useful to have the
"read-only" idea around. So port it back to GitLab CE.

Also having the principle of read-only in GitLab CE would hopefully
lead to less errors introduced, doing write operations when there
aren't allowed for read-only calls.

Closes gitlab-org/gitlab-ce#37534.

Closes #38808