Need a little help on repo sync issue

[Dr. H. Nikolaus Schaller]

After I did sync successfully yesterday and was able to compile everything,
I did a new repo sync today but it fails with this error:

iMac:replicant-4.0 hns$ ../tools/repo sync
Fetching projects: 100% (280/280), done.  
Syncing work tree:  98% (275/280)  error: Your local changes to the following files would be overwritten by checkout:
	prebuilt/common/apps/FDroid.apk
Please, commit your changes or stash them before you can switch branches.
Aborting
Syncing work tree: 100% (280/280), done.  

error: vendor/replicant/: replicant/vendor_replicant checkout 8d71e23c977a7e946ee8aed41572b8fdfaeb2185 
iMac:replicant-4.0 hns$ ls -l prebuilt/common/apps/FDroid.apk
ls: prebuilt/common/apps/FDroid.apk: No such file or directory
iMac:replicant-4.0 hns$ ls -l prebuilt/common/apps
ls: prebuilt/common/apps: No such file or directory
iMac:replicant-4.0 hns$ ls -l prebuilt/common
total 0
drwxr-xr-x  2 hns  hns  238  1 Jul 19:39 ant
drwxr-xr-x  2 hns  hns  238  1 Jul 19:39 asm
drwxr-xr-x  2 hns  hns  272  1 Jul 19:39 commons-compress
drwxr-xr-x  2 hns  hns  272  1 Jul 19:39 ddmlib
drwxr-xr-x  2 hns  hns  204  1 Jul 19:39 ecj
drwxr-xr-x  2 hns  hns  306  1 Jul 19:39 eclipse
drwxr-xr-x  2 hns  hns  374  1 Jul 19:39 groovy
drwxr-xr-x  2 hns  hns  408  1 Jul 19:39 http-client
drwxr-xr-x  2 hns  hns  170  1 Jul 19:39 jarjar
drwxr-xr-x  2 hns  hns  340  1 Jul 19:39 jfreechart
drwxr-xr-x  2 hns  hns  272  1 Jul 19:39 jython
drwxr-xr-x  2 hns  hns  306  1 Jul 19:39 kxml2
drwxr-xr-x  2 hns  hns  204  1 Jul 19:39 layoutlib_api
drwxr-xr-x  2 hns  hns  170  1 Jul 19:39 mkidentity
drwxr-xr-x  2 hns  hns  272  1 Jul 19:39 netbeans-visual
drwxr-xr-x  2 hns  hns  204  1 Jul 19:39 ninepatch
drwxr-xr-x  2 hns  hns  238  1 Jul 19:39 osgi
drwxr-xr-x  2 hns  hns  170  1 Jul 19:39 pc-bios
drwxr-xr-x  2 hns  hns  238  1 Jul 19:39 swing-worker
drwxr-xr-x  2 hns  hns  204  1 Jul 19:39 tools-common
drwxr-xr-x  2 hns  hns  204  1 Jul 19:39 tradefed
iMac:replicant-4.0 hns$ 

The strange thing is that I don't even have the file the error message is complaining about i.e. there is nothing to overwrite...
But the apps directory is missing.
A git status within prebuilt/common tells that there is no branch and nothing uncommitted.

Any hints what I should do?

-- hns