What steps will reproduce the problem?

mkdir annex_stress; cd annex_stress, then execute the following script:

#! /bin/sh

# creating a directory, in which we dump all the files.
mkdir probes; cd probes

for i in `seq -w 1 25769`; do
    mkdir probe$i
    echo "This is an important file, which saved also in backup ('back') directory too.\n Content changes: $i" > probe$i/probe$i.txt
    echo "This is just an identical content file. Saved in each subdir." > probe$i/defaults.txt
    echo "This is a variable ($i) content file, which is not backed up in 'back' directory." > probe$i/probe-nb$i.txt
    mkdir probe$i/back
    cp probe$i/probe$i.txt probe$i/back/probe$i.txt

It creates about 25000 directory and 3 files in each, two of them are identical.

What is the expected output? What do you see instead?

I expect git annex could import the directory within 12 hours. Yet, it just crashes the gui (starting webapp, uses the cpu 100% and it does not finish after 28hours.)

What version of git-annex are you using? On what operating system?

version 2013.04.17

Please provide any additional information below.

I do hope git-annex can be fixed to handle large number of files. This stress test models well enough my own directory structure, relatively high number of files relatively low disk space usage (my own directory structure: 750MB, this test creates 605MB).

Best, Laszlo