Ok, since I'm the only talking in this thread (is the keyword "Java" the 
problem around here?), I'll describe what I did to "kinda" get it to work.

Using an webapp directory, generated or not by Maven, I have the following 
structure:

root (war)
| - WEB-INF
|   | - classes (directory with bytecode data)
|   | - lib (jars)
|   | - web.xml
|   | - appengine-web.xml
|   | - (other config files)
| - static files, such as htmls, images and so on
| - folders with static files as well

When using appcfg.sh to update my application, it copies the entire 
structure to a temporary folder, and then starts the upload of files.

The structure of the temporary folder is sightly different from the 
original folder:

root (temp)
| - WEB-INF
|   | - classes (directory with bytecode data)
|   | - lib (jars)
|   | - web.xml
|   | - appengine-web.xml
|   | - (other config files)
| - __static__
    | - static files, such as htmls, images and so on
    | - folders with static files as well

So, in other words, it copies all static files and folders to a 
"__static__" directory. Nothing fancy so far.

The problem is, in my setup, I don't know why, the appcfg.sh is generating 
symbolic links of the static files at the root temporary folder. Something 
like this:

root (temp)
| - WEB-INF
|   | - *
| - __static__
|   | - image.png
|   | - index.html
| - image.png -> /home/user/workspace/myapp/myapp-war/target/image.png
| - index.html -> /home/user/workspace/myapp/myapp-war/target/index.html

So I thought: why the heck does it need these symbolic links AND the 
__static__ folder?

And then I made one of worst workarounds with the poorly supported 
Maven-Java-App-Engine-Modules so far: after running "appcfg.sh update 
myapp", I paused the process (ctrl+z) right after it created the temporary 
folder, and right before it started scanning the files. With the paused 
process, I went to the temp folder and removed all those weird symbolic 
links, leaving only the __static__ and the WEB-INF directories. After that, 
I resumed the process (fg), and there you go, problem solved.

I don't know if it is a bug, but it is a really annoying situation.

Next time I'll fake my input to look like python's to see if I get some 
support =P

See you.

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