Better ignore setup for avoiding clobbering internal files and ignored files

[sdleffler]

At current we use ignore::WalkBuilder and set it to depth of 1 for walking single directories. This is a bit of a hack. In any case, this also results in ignoring some things that Git will actually not ignore changes to (the .attaca directory, for example, will show up in a git status.) A precise sequence of overrides should be figured out in order to cause the WalkBuilder to ignore only Attaca/Subito-specific files.