Sometimes force-dedupe-git-modules hangs when used with npm's postinstall and prints errors like these:
preserving git-based module: my_module at .
npm ERR! cb() never called!
npm ERR! not ok code 0

This is usually solved by running npm install multiple times.

There are problems with latest npm releases, namely version 2.1.18. It appears that npm has changed the format of the _from field of installed package.json files. Sometimes npm installs a package from the npm cache and adds something like "c:\temp\npm\cache" (the path is just from memory) to the _from field. In these cases the _resolved field has something like "git://foobar".

If a git reference of a winston transport (e.g. winston-couchdb) is used, the application stops working properly, since winston-couchdb is moved to the root, while the winston module might be located elsewhere in the node_modules tree. winston-couchdb tries to require winston, but it's not found, since it's not a dependency of winston-couchdb (it's a devDependency).

Making winston a dependency of winston-couchdb would fix the exception, but doesn't fix the issue, as winston transports seem to make a singleton assumption.

This might be a winston problem more than a force-dedupe-git-modules problem, though.

EDIT: Also the cradle module is a problem. The tree structure is something like this:
root\node_modules\sub\node_modules\cradle
root\node_modules\sub\node_modules\winston
root\node_modules\sub\node_modules\winston-couchdb

.. and after force-dedupe-git-modules
root\node_modules\sub\node_modules\cradle
root\node_modules\sub\node_modules\winston
root\node_modules\winston-couchdb

Since winston-couchdb requires cradle, an exception is thrown. cradle is not installed to winston-couchdb in the first place, as it can be found from the parent directory.