parse flags

[mxmxchere]

• Make version a flag, otherwise the other flags are not parsed correctly
• Rename manifest variable that holds index to index

[nkraetzschmar]

what exactly is the problem with parsing the other flags when version is a positional arg? Parsing worked fine in my tests.

If there is no good reason I'd prefer keeping version as a positional arg since it is the only required flag and in almost all cases this is the only one that should be provided. All others are only for special corner cases to overwrite the defaults.

For 99% of use cases the update tool will probably be called simply as gardenlinux-update {version}, so always requiring to call it as gardenlinux-update --version {version} would be undesirable.

[mxmxchere]

I should have read the docs of flag.Arg and flag.NArg. They are referring to args that are left after flags are parsed. I thought they refer to the strict index command line arguments are supplied with. My mistake, this PR is no longer needed.