User installs should be able to overwrite tool symlinks created by root installs

[Chumper]

When a root installs a tools the symlink in /usr/local/bin will have the mode 755 set.
This prevents user installs to overwrite symlinks when a user installs a tool.

We should change this to be 775 on created symlinks,

[Chumper]

The problem is not the symlink, but rather the shell wrapper.
The symlinks permission does not really matter:

Symlinks are always world readable/writeable.

from https://askubuntu.com/questions/1145107/mysql-server-config-file-permissions-on-ubuntu-18-04/1145114#1145114

The shell wrapper on the other hand is basically just a shell script and needs proper permissions.
For the case with python this needs a fix in the python tool, for all other tools in the utils/linking.sh.

[viceice]

Ok, so it seems we should always use shell wrapper scripts to not need change the target files.

[Chumper]

So no symlinks then?
We will always create a small shell script that simply calls the correct binary in the correct path?
We can do that.
In that case we would utilize shell_wrapper and export_tool_env more.

[viceice]

what about writing the shell wrapper as root only on prepare stage, and write the tool version to call to /opt/..., so the wrapper simply reads version and calls real binary. 🤔

That way we won't need to make /usr/local/bin writable to users, as we don't need to overwrite the wrapper.

@rarkins WDYT? This would be again a major change and propably would allow us to solve #101

[Chumper]

So you would write all shell wrappers during the prepare phase?
Or how does it work when we have a tool that is installed during runtime?

The prepare phase for me is that a tool that is installed as root can prepare runtime installation of this tools as well if possible which does not need root rights.
So it is called for each tool initially on each root install for that tool and possibly there is no prepare phase if the tool is never installed as root.

Is the prepare phase for you something that will be called during creation of the docker image for all tools instead?