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If you're managing dotfiles with Make (which I attempted once...) then may I direct you to GNU Stow instead? It's much easier to manage a bunch of files centrally and just symlink to them all:

http://brandon.invergo.net/news/2012-05-26-using-gnu-stow-to...

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The problem I seem to be having with various dotfiles tools is they seem to be doing too much, where a script with a bunch of calls to ln -s would do.

May I introduce you to dircombine? Take multiple directories full of dotfiles and symlink them all into another directory.

http://git.kitenet.net/?p=joey/home.git;a=blob_plain;f=bin/d...

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