Scenario: I\'m trying to get my unix dot-files under git. I have to work between (at least) the cygwin environment and some standard linux distros (ubuntu a
For that particular case, where there is a lot of common files evolving in one branch, and only a few config files specific per environment... we do not store the config file in Git. At all.
We do store template of said config files, plus all the specific per-environment values, plus a script able to replace the variables in the template files by the correct value (detecting the current platform)
That way, we do not need to make a branch only for those files.
Another good way to manage those kind of files (with a platform-specifc content) is through a git attribute filter driver (see also Pro Git book).
A filter driver consists of a
cleancommand and asmudgecommand, either of which can be left unspecified.
Uponcheckout, when thesmudgecommand is specified, the command is fed the blob object from its standard input, and its standard output is used to update the worktree file.
Similarly, thecleancommand is used to convert the contents of worktree file upon check-in.
That way, a script (managed with Git) referenced by the smudge can replace all the variables by platform-specific values, while the clean script will restore its content to an untouched config file.

The main idea remains: avoid creating branches only for that kind of parallel evolution.