correct workflow with bare repo and pull?

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Myself and the other developer on the team have private repos, and we
push to a bare repo (which we use for Hudson builds).  For now we only
use the master branch.  No other remote repos.  When another developer
pushes changes to the bare repo, and I pull them, all of the files they
pushed show up as modified on my box when I do "git status" (even
though I had not modified them).  How to avoid this?   Also, one
developer saw really strange results when they did a "git pull origin
master" and "git status" -- the paths shown below do not exist in the
local work area.  These files have always lived under a-core/.... so it
is really odd that they show up under a-web
# On branch master
# Changes to be committed:
#   (use "git reset HEAD <file>..." to unstage)
#
#    new file:   a-web/src/main/java/com/blah/account/Account.java
#    new file:   a-web/src/main/java/com/blah/account/AccountType.java
#
# Changed but not updated:
#   (use "git add/rm <file>..." to update what will be committed)
#   (use "git checkout -- <file>..." to discard changes in working directory)
#
#    deleted:    a-web/src/main/java/com/blah/account/Account.java
#    deleted:    a-web/src/main/java/com/blah/account/AccountType.java

What are we doing wrong?  


      
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