Directory comparison of Git branches

This (comparing directories instead of file-by-file) should be available soon:
See [ANNOUNCE] Git 1.7.11.rc1:

"git difftool" learned the "--dir-diff" option to spawn external diff tools that can compare two directory hierarchies at a time after populating two temporary directories, instead of running an instance of the external tool once per a file pair.

See "Patch difftool: teach difftool to handle directory diffs", from this fork of git:

When 'difftool' is called to compare a range of commits that modify more than one file, it opens a separate instance of the diff tool for each file that changed.

The new '--dir-diff' option copies all the modified files to a temporary location and runs a directory diff on them in a single instance of the diff tool.

It sounds like you've already figured out the right answer -- use git clone and git checkout to set up a directory to compare to, then run BCompare.exe. The below script might be a good starting point.

#!/bin/sh
(                              # execute in a subshell so you can continue
                               #   working in the current shell
    set -o xtrace              # bash setting that echos each command before it's executed
    > /tmp/auto_bcompare_log   # truncate existing log file
    BRANCH="$1"                # get branch argument from command line
    TEMPDIR=`mktemp -d`        # get a temp directory
    CWD=`pwd`                  # remember the current directory
    git clone $CWD $TEMPDIR
    cd $TEMPDIR
    git checkout $BRANCH
    cd $CWD
    BCompare.exe $CWD $TEMPDIR
    rm -rf $TEMPDIR
) >> /tmp/auto_bcompare_log 2>&1 < /dev/null & # background and redirect
                                               # stdout/stderr/stdin