Using Git on Windows, behind an HTTP proxy, without storing proxy password on disk

since git 2.8.0

git config --global http.proxy http://[user]@proxyhost:port
git config --global credential.helper wincred

Instead of using git setting, you can also use environment variable (that you can set just for your session), as described in this answer:

set http_proxy=http://username:password@proxydomain:port
set https_proxy=http://username:password@proxydomain:port
set no_proxy=localhost,.my.company 

So your wrapper script could, instead of modifying the .gitconfig (and leaving your password in plain text) set environment variables on demand, just for your current session.

As noted by Welgriv, this is unsafe since environmental variables can be accessed by any program in user mode.

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These days (2020, 5+ years later), I prefer:

set http_proxy=http://127.0.0.1:3128
set https_proxy=http://127.0.0.1:3128

With 127.0.0.1:3128 being the default URL for a genotrance/px, a small HTTP proxy server, which will automatically authenticate through an NTLM proxy.
No password or even user to set.

VonC's answer doesn't always solve the problem. I don't know why, but it may depend on the proxy server - or maybe it's some other issue alltogether?

It may help to replace the git:// protocol of the repository with http://.

Note: As in VonC's answer, you'll have to setup the http(s)_proxy environment variables first:

set http_proxy=http://username:password@proxydomain:port
set https_proxy=http://username:password@proxydomain:port

For example, clone marble's stable git would usually be cloned like this (from the marble documentation):

git clone -b Applications/15.12 git://anongit.kde.org/marble ~/marble/sources

In windows' cmd (assuming http_proxy has been set), you may then have to use http[s]:// instead:

git clone -b Applications/15.12 http://anongit.kde.org/marble ~/marble/sources