Fixes to flatpak-cargo-generator

[zecakeh]

Various errors I encountered while trying the script and then to build a Flatpak app.

See each commit message for details.

See the last commit of flathub/org.gnome.Fractal#41 for the differences in the generated sources.

[hfiguiere]

I wonder how this intersects with #323 and #325.

[hfiguiere]

and also #399

[hfiguiere]

And issue #367, seems that this would fix it.

[zecakeh]

After checking all of those:

• There is no direct link/conflict with cargo: Handle excluded paths in workspaces #323, although I don't recommend to merge it (in favor of Find all crates in git repositories, matching cargo's behavior #399).
• There is no direct link/conflict with cargo: Allow filtering packages by name #325, which looks fine.
• The last commit of this PR is not necessary if Find all crates in git repositories, matching cargo's behavior #399 is merged (which I recommend over cargo: Handle excluded paths in workspaces #323).
• It could possibly fix cargo generator cant seem to find build-dependencies #367, if we knew what the actual error looks like, and if we could reproduce it.

[zecakeh]

I rebased on master and dropped the last commit, to fix conflicts.

[hfiguiere]

thanks!