This should now be fixed.

The problem is that SFI embeds Javascript directly in the HTML. Now that jQuery is loaded late it is not (always) available in time for the SFI inputs.

Elements on the NavBar have an ID, e.g. n-mainpage-description or ca-talk.
These should additionally be available as classes, but otherwise... whatś missing?

The NavBar was overhauled in Chameleon 1.2, so I think this should be fixed. If not, re-open please.

Usually I do, apparently I forgot this time. Sorry about that.

Getting this as well when calling .../Special:FormEdit/SomeForm

This is included now in the latest version (1.1.4) of the Bootstrap extension.

I don't think this can be done without major effort. Autoedit uses the SF API module. If you open it for autoedit you open it for everything. It's not enough to just add a new parameter 'fromAutoedit' to the API. Any bot can send that.
Furthermore we would have to find a way to "convince" EditPage to force a save against the hook error from ConfirmEdit.

Guess so (There is no really good German translation of "Main", which may have contributed to this issue):
https://github.com/wikimedia/mediawiki/blob/master/languages/i18n/de.json#L2024

Have you tried calling the namespace Projekt? Also, it may be called something different entirely (although I doubt that if Project works when switching to English). See the namespace selector on Special:AllPages for a list of valid namespace names on your wiki.

No, I don think so. The newer compiler was intended to be a drop-in replacement after all. But it should be rather straightforward. I started it once and it boiled down to replacing one compiler with the other and fixing the compiler errors. The problem was that MW used user-defined functions, which the new compiler did not support back then. It does now. Also, MW does not use these functions anymore, as far as I know. The rest should really mostly be cleaning up the include paths in the less files.

No. There are two classes named lessc, one provided by the lessc package, the other provided by the less.php package. The lessc package was there first, but it is not maintained any more. The less.php package includes a lessc class as an adapter to make it easier to migrate away from lessc. The result is that we now have two packages both providing a lessc class.

The issue is, that less.php includes its own lessc class so it can be used as a drop in replacement for the lessc compiler. It's only recently that composer actually checks for duplicate class definitions. Anyway, it should not be a problem as long as the lessc compiler is loaded first (which seems to be the case), so it is available for MW core. The Bootstrap extension itself does not use the lessc class. In fact, before composer checked for this, Bootstrap removed the duplicate lessc class itself to ensure compatibility with MW (https://github.com/wikimedia/mediawiki-extensions-Bootstrap/blob/master/src/Hooks/SetupAfterCache.php#L113).

The link on the logo is built in Logo.php. See https://github.com/wikimedia/mediawiki-skins-chameleon/blob/master/src/Components/Logo.php