Notes

This should be obvious after you think of it, but it is a honest mistake and cleaning up the mess afterwards can cause you big problems, so here it is:

Running some_command --base=~/Sites/dir is very different from some_command --base ~/Sites/dir

The extra = makes all the difference. With it, the ~/ is not expanded to your $HOME by the bash shell, so if your some_command uses that path as a base directory, you'll end up with a new path like ./~/Sites/dir.

This means that in your current working directory, you'll have a subdirectory named ~, and you might be tempted to just rm -rf ~ to clean it up...

I think that we can all agree that a rm -rf ~ command would be disastrous (the correct command would be rm -rf ./~), so please be careful when using options with parameters. The = will disable shell expansion, and you could end up in a bad place.