Today I got this for a change trying to update via Composer:
[RuntimeException] Failed to execute git checkout 'f7543bcb7ad1b08c1924d65aeea9e353d5953381' -- && git reset --hard 'f7543bcb7ad1b08c1924d65aeea9e353d5953381' -- error: The following untracked working tree files would be overwritten by checkout: tests/phpunit/Integration/ByJsonScript/Fixtures/p-0408 [#1252] intext to use non-strict mode.json Please move or remove them before you can switch branches. Aborting
- Solution
Go to the directory "/extensions", do a rm -r SemanticMediaWiki/
there, go back to wiki root "/w" and do the composer update --prefer-source --no-dev
See also issue 1351 on GitHub.