It looks like the mapfiles are not being 'git add'ed after changes.

$ mkdir BEtest
$ cd BEtest
$ git init
$ be set-root .
$ be new 'new'
$ git status
# On branch master
#
# Initial commit
#
# Changes to be committed:
#   (use "git rm --cached <file>..." to unstage)
#
#       new file: .be/bugs/8f021d79-44f5-479f-af12-c37e2caf3ce1/values
#       new file: .be/settings
#       new file: .be/version
#
# Changed but not updated:
#   (use "git add <file>..." to update what will be committed)
#
#       modified:   .be/bugs/8f021d79-44f5-479f-af12-c37e2caf3ce1/values
#       modified:   .be/settings
#