Improve autoupdate round 4

[lldelisle]

Sorry I found again unexpected behaviours:

• Here the comment says that there are new updates while the new updates are for another tool: Updating tools/agat from version 1.4.0 to 1.4.1 bgruening/galaxytools#1507 (comment)
• Here the comment says to delete the branch while it has been deleted: Updating tools/rna_tools/ribotaper from version 1.3.1a to 1.3.1 bgruening/galaxytools#1242 (comment)

[lldelisle]

Another unexpected behaviour see galaxyproject/planemo#1478

[lldelisle]

Another 'failure': because of | tee to write stderr to file, the exit code of this command is always 0, even if the planemo autoupdate had an exit code of 1. I added set -o pipefail to keep an exit code of 1.

[bgruening]

The bot is saying I should remove the branch, but I have bgruening/galaxytools#1354 (comment)

[lldelisle]

Yes, this will be solved by 3085c45

[lldelisle]

May I merge this? @nsoranzo @mvdbeek