How do I clean all git history and blobs of files not currently present in HEAD with BFG

Question

I want to clean all blobs and history of files that have been previously deleted (ie no longer present in HEAD), I am currently running these commands, but BFG seems deleting all blobs, including those present in HEAD:

git log  # Returns 1050 commits
git commit -a -m "Clean the old history and blobs with BFG"
java -jar bfg.jar --delete-files '*'  # Delete all files not in HEAD
git log  # Still returns 1050 commits, all empty
git diff 5458b2^ 5458b2  # Returns 0 change, while it concerns a protected file

BFG actually took into account the protected files in HEAD, like gitignore for example:

Protected commits
-----------------
These are your protected commits, and so their contents will NOT be altered:
 * commit 22a1ebd3 (protected by 'HEAD') - contains 1451 dirty files : 
    - .gitignore (813 B)
    - ...

But they are removed anyway, while they are supposed to be protected:

Deleted files
-------------
    Filename     Git id  
    ----------------------------------------
    .gitignore | 091217cf (672 B), 17e3d7c5 (227 B)...                          

Answer 1

I am finally using that script to clean up the repository from obsolete deleted files. It combines several steps of branch rewritings and garbage collector call to clean the current repository.

I managed to compress a 700MB heavy repo in a 4MB fresh repository. As usual, duplicate your repository before running this kind of script, it might result in some lost of data!

Answer 2

Maybe you can try the following command to delete all unreachable objects.

git prune

or

git gc