Tidy up init process

[thespad]

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• I have read the contributing guideline and understand that I have made the correct modifications

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Description:

• Renamed a few steps to clarify that they're part of the swag init and not related to the base - previously we had things like init-permissions on the base and then init-permissions-config in swag, it's now init-swag-permissions.
• Updated init steps to depend on init-config not init-nginx-end (init-config already depends on init-nginx-end)
• Removed unnecessary chmod +x for le-renew.sh (it's now +x in the repo)
• Disabled CI test as we were just fake OKing it as the first init step after the base so it doesn't really test anything

Benefits of this PR and context:

How Has This Been Tested?

Source / References:

[LinuxServer-CI]

I am a bot, here is the pushed image/manifest for this PR:

ghcr.io/linuxserver/lspipepr-swag:3.0.1-pkg-c8ade9f4-dev-ed7c58a4c345a043c3f68ab97986565904a7a142-pr-521

[quietsy]

LGTM