The first page should be the starting point from which to start. Building a story is a little bit difficult because there are a lot of different use cases. I also thought it would be good to have a chapter-like manual with links to previous and next pages but that's hard to maintain.

What I meant is: You don't need a FileZilla Server on your Win7 Host. You just need an FTP-Client that can SFTP into the debian6 VM. There is already an OpenSSH Server running that will accept the SFTP requests. This way you push your files into the VM, as you try to pull the files into the VM. With my approach you don't need to enter commands inside the VM.

That is true for all the technical documentation about software, can you be more specific?

No it's not.

- download the boinc source using git on Win7 (done)
- copy the Windows example files (including boinc_samples.sln) (done)
- Compile this modified version in Win7 (using visual Studio!) (works for 32-bit, but having problems with getting the version for 64-bit)
I ment visual studio, but wrote visual basic by mistake
- Connect to the server in my debian6 VM using FileZilla Client (sftp) and put the .exe file in the correct directory (filezilla server has been configured and is ready to be contacted)
- run the appropriate commands inside the debian6 VM to update the applications (I think the commands that you are referring to are 'bin/xadd' and 'bin/update_versions' if I'm correct)

And of course my usual questions:
- What's your programming / Linux experience?
Programming is okay I guess. Very decent skills in Java and halfbaked in C++.
My Linux experience is limited to this debian6 VM.
- What kind of application do you want to run?
I simply want to modify the u2.cpp to have a different function.
The classical version converts a string of characters to upper case, but
the modified application will calculate the factorial of a given number (given in the input file). I have already modified the sample_work_generator to fit my needs. (which was surprisingly easy using the make command)
- What documentation did you read before posting?
I have read the following documents before posting:
- http://boinc.berkeley.edu/trac/wiki/CompileApp (only after noticing that the wrapper didn't fit my needs)
- http://boinc.berkeley.edu/trac/wiki/WrapperApp (turned out to be useless)
- the quickstart page
- http://boinc.berkeley.edu/trac/wiki/DesktopGrid
- http://boinc.berkeley.edu/trac/wiki/ServerIntro
- http://boinc.berkeley.edu/trac/wiki/VmServer
- a whole bunch of others that were of lesser importance

- Any suggestions for improving the documentation?
It is in my opinion very noob-unfriendly, which scares newbies away. After getting a lil bit accustomed to BOINC it is a lot better, but stays unclear.
Regards
Christian

In order to build your own windows executables you either need Visual Studio or mingw to cross compile.

If you already have an .exe file and want to use the wrapper feature you can use the SSH service in the debian6 VM to insert your files. Just use an FTP-Tool like Filezilla and connect using the SFTP Protocol. Username and Passwort is the same as you login with. Information is available on the page you linked to in your post.

BOINC IS ENABLED

DAEMON pid     status     lockfile disabled commandline
 1     1298  running      locked     no     feeder -d 3
 2     1300  running      locked     no     transitioner -d 3
 3     1302  running      locked     no     file_deleter -d 3
 4     1304  NOT RUNNING UNLOCKED    no     sample_work_generator -d 3
 5     1306  running      locked     no     sample_bitwise_validator -d 3 --app example_app
 6     1308  running      locked     no     sample_assimilator -d 3 --app example_app

(Also a list of tasks)

2013-03-18 08:46:16.1530 [CRITICAL] can't read input template templates/example_app_in.xml

example_app: example Application
---------------------------------
No homogeneous redundancy. Weight 1.
Versions:

   224.89 windows_intelx86
   224.89 windows_x86_64
   224.89 i686-pc-linux-gnu
   ... (and so on)
   242.53 windows_intelx86

No work available at the moment