Please add support for INPUT_PULLUP

The arduino core files support INPUT_PULLUP as an argument to pinMode().  Mighty-1284p didn't.  This pull request adds support for it.

It also explicitly disables the pullup if INPUT is used, which is the same as in the official Arduino files.

The request includes a commit to clean up permissions: many source files were marked as executable.  While this is harmless, it is also pointless.