Yes, by setting --git-dir and --work-tree to the appropriate settings.

The attached Bash alias (function ogit()) does this for you.

'ogit' is a wrapper for 'git', call it almost exactly like you would call 'git'. The only thing that has been added is the command "ogit use", which designates the ogit repo that you will use for all future 'ogit' calls:

$ ls -lA
drwxr-xr-x  8 dee      dee      4096 Feb 27 16:37 .git.one.txt/
-rw-r--r--  1 dee      dee        10 Feb 27 16:11 one.txt
-rw-r--r--  1 dee      dee        26 Feb 27 16:39 two.txt

$ ogit
You must first set a OneGit repository first, using 'ogit use <filename>'

$ ogit use ./two.txt
Initialized empty Git repository in /home/dee/docs/.git.two.txt/
OneGit is now using:  ./two.txt

$ ls -lA
drwxr-xr-x  8 dee      dee      4096 Feb 27 16:37 .git.one.txt/
drwxr-xr-x  8 dee      dee      4096 Feb 27 16:42 .git.two.txt/
-rw-r--r--  1 dee      dee        10 Feb 27 16:11 one.txt
-rw-r--r--  1 dee      dee        26 Feb 27 16:39 two.txt

$ ogit status
# On branch master
#
# Initial commit
#
# Untracked files:
#   (use "git add ..." to include in what will be committed)
#
#       two.txt
nothing added to commit but untracked files present (use "git add" to track)

$ cat .git.two.txt/info/exclude
*
!two.txt

$ ogit add two.txt

$ ogit commit -m 'initial commit'
Created initial commit d39b940: initial commit
 1 files changed, 1 insertions(+), 0 deletions(-)
  create mode 100644 two.txt

$ ogit log
commit d39b940066a130f1cbd597280056d9c5aa7d637e
Author: Dee Newcum
Date:   Mon Feb 27 16:42:06 2012 -0500

    initial commit

$ ogit use ./one.txt
OneGit is now using:  ./one.txt

$ ogit log
commit 2db7a4d5299584fae9af50bfd91f66fd888d4abf
Author: Dee Newcum
Date:   Mon Feb 27 16:29:25 2012 -0500

    initial commit