No, I don't. I just ran the checks now with this PR as I thought it might help.
The tests fail in the same way for Geany master, so you are absolutely right: it's not new and not related to this PR.

Ctags uses appveyor for CI on Windows so it might be worth considering to use it as well so we can run tests for Windows builds too.

We discussed this in #1241.
I still don't want to invest time in an appveyor setup.
Some time ago I started (and not yet finished) a dockerized MSYS2 setup to cross-build Geany
and Geany-Plugins from GIT to release ready installers. The script and Docker container could also be used in a Travis CI step even though my primary target are nightly build installers and especially release installers without booting a Windows machine.

1. Would you try opening the file in binary mode and check what tests fail when you do?

No change.

Weird, I don't get it then. This is the place where tags are written and newlines are written using \n - so it's a matter of figuring out why \n produces CRLF.

I gave it another shot: the binary didn't work because of my other change in runner.sh where I added --strip-trailing-cr to the diff command.
The good news is: without the --strip-trailing-cr change, the binary mode actually fixes all the tests except the six failures. The six failures can be fixed easily by converting the test samples to LF, however.
So it should be pretty easy to get the tests running on Windows as well.

1. Would you try changing CRLF line ends in the SQL tests that fail to LF to see if this is the reason for the problem? I checked uctags implementation of file reading and CRLF should be handled there correctly so it could be something parser-specific.

This actually helps. I converted the test files of the six failures to LF and the tests passed fine.

Good, at least we know it's the CRLFs. Now only to figure out why. I'm afraid I'm out of ideas so it's your turn with debugging :-(

See above :).

So I think we should address this separately, maybe after this PR got merged.

Sounds good to me.

I just opened #2677 for this.

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