Cogito and --exclude vs --exclude-per-directory

[Note: this experiment was done with git 0.99.9g and Cogito 0.15.1, so ]

It seems that --exclude patterns always take precedence over --exclude-per-directory patterns. For example:

  $ ls -a
  ./  ../  .bar  bar.txt  .foo  foo.txt  .git/  .gitignore

  $ cat .gitignore
  !.bar

  $ git-ls-files -o --exclude='.*' --exclude='!.bar'
  .bar
  bar.txt
  foo.txt

  $ git-ls-files -o --exclude='.*' --exclude-per-directory=.gitignore
  bar.txt
  foo.txt

Is this the intended behavior?

Since Cogito specifies a few "default" ignore patterns with --exclude, (such as .* and *.o) these become impossible to override with ! patterns in .gitignore files. In effect, the default patterns are given priority over user-supplied patterns.