Do not use gitignore if explicitly passing excludes (#2170)

Closes #2164.

Changes behavior of how .gitignore is handled. With this change, the rules in .gitignore are only used as a fallback if no exclusion rule is explicitly passed on the command line or in pyproject.toml. Previously they were used regardless if explicit exclusion rules were specified, preventing any overriding of .gitignore rules.

Those that depend only on .gitignore for their exclusion rules will not be affected. Those that use both .gitignore and exclude will find that exclude will act more like actually specifying exclude and not just another extra-excludes. If the previous behavior was desired, they should move their rules from exclude to extra-excludes.