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@languitar: That makes more sense. So like this:
if [ $_gtkver == 'gtk3' ]; then
#ln -s "${prefix}/DocFetcher-GTK3.sh" "${prefix}/DocFetcher.sh"
ln -s "/usr/share/${pkgname}/DocFetcher-GTK3.sh" "${prefix}/DocFetcher.sh"

makepkg doesn't seem to complain about it.

No wait. The problem is that the symlink originates from <thebuilddir>/usr/share... Instead, it must be from /usr/share to $prefix/use/share..., while ignoring the warning that the source file doesn't exist (yet, before the package is installed).

@languitar: do you mean replace all instances of ${prefix} in the package() section with ${pkgdir}/usr/share/${pkgname}?
I can do that. Is it always bad to use a variable to simplify typing paths in package() then?

Seems to be caused by using prefix as a variable. It should probably be pkgdir instead.

I see the problem:

languitar@jaco ~/sciebo/literature/Citavi/thesis/Citavi Attachments> pacaur -Ql docfetcher | grep \\.sh
docfetcher /usr/share/docfetcher/DocFetcher-GTK2.sh
docfetcher /usr/share/docfetcher/DocFetcher-GTK3.sh
docfetcher /usr/share/docfetcher/DocFetcher.sh
languitar@jaco ~/sciebo/literature/Citavi/thesis/Citavi Attachments> which docfetcher
/usr/bin/docfetcher
languitar@jaco ~/sciebo/literature/Citavi/thesis/Citavi Attachments> docfetcher
/usr/bin/docfetcher: line 3: /usr/share/docfetcher/DocFetcher.sh: No such file or directory
languitar@jaco ~/sciebo/literature/Citavi/thesis/Citavi Attachments [127]> cat /usr/share/docfetcher/DocFetcher.sh
cat: /usr/share/docfetcher/DocFetcher.sh: No such file or directory
languitar@jaco ~/sciebo/literature/Citavi/thesis/Citavi Attachments [1]> ll /usr/share/docfetcher/
total 76K
drwxr-xr-x 2 root root 4.0K Jan 10 16:36 conf/
drwxr-xr-x 3 root root 4.0K Jan 10 16:36 DocFetcher.app/
-rw-r--r-- 1 root root 30K May 16 12:34 docfetcher-daemon-linux
-rwxr-xr-x 1 root root 310 Jan 10 16:36 DocFetcher-GTK2.sh*
-rwxr-xr-x 1 root root 291 Jan 10 16:36 DocFetcher-GTK3.sh*
lrwxrwxrwx 1 root root 95 May 16 12:34 DocFetcher.sh -> /home/languitar/.cache/pacaur/docfetcher/pkg/docfetcher/usr/share/docfetcher/DocFetcher-GTK3.sh
drwxr-xr-x 5 root root 4.0K Jan 10 16:36 help/
drwxr-xr-x 2 root root 4.0K Jan 10 16:36 img/
drwxr-xr-x 2 root root 4.0K Jan 10 16:36 indexes/
drwxr-xr-x 2 root root 4.0K Jan 10 16:36 lang/
drwxr-xr-x 3 root root 4.0K May 16 12:34 lib/
drwxr-xr-x 2 root root 4.0K May 16 12:34 misc/

It seems the symlink for DocFetcher.sh is corrupted and the build environment seems to leak into the creation of that link.

@languitar I'm not sure what you mean. It all works for me still. /usr/share/docfetcher/DocFetcher.sh is in the package still and the 'docfetcher' script works. What are you seeing?

The included docfetcher script doesn't work anymore as the references script in the package has gone

KDE should have nothing to do with variables in a shell script. I'm setting the value of $_gtkver to be 'gtk3' by default. It's only there so people have the choice of using GTK2 or 3. It's strange that you get no shortcut.

I'll have a closer look at the script tonight.

I had to do the following fixes:

sudo chmod 655 /usr/share/docfetcher/DocFetcher-GTK*
sudo ln -s /usr/share/docfetcher/DocFetcher-GTK2.sh /usr/share/docfetcher/DocFetcher.sh
sudo sed -i s,"Icon=docfetcher","Icon=/usr/share/docfetcher/img/docfetcher128.png", /usr/share/applications/docfetcher.desktop
sudo sed -i s,"Name=Docfetcher","Name=DocFetcher", /usr/share/applications/docfetcher.desktop

The first one is already in http://hastebin.com/arubabakoq.bash, the second one can easily be fixed there.
The third (no icon) and fourth (typing error) can easily be fixed in the desktop file.

Thanks!

@http://hastebin.com/arubabakoq.bash

I use kde, so $_gtkver gives nothing (at least on my system).

So there is no link made.