Given a.out containing compiled binary of the example class from https://github.com/LibertyEiffel/Liberty/pull/183 :

== Option order is important

$ ./a.out -f John -l Doe -e "Book title" 2000
-- is invalid because of the -e, but why?

$ ./a.out -f John -e -l Doe "Book title" 2000
-- crashes

$ ./a.out -e -f John -l Doe "Book title" 2000
-- seems to be the only accepted order to pass the -e option

== Short option grouping

$ ./a.out -ve -f John -l Doe "Book title" 2000
-- -v is processed (program displays verbosity level), -e ignored (program doesn't print the "ed." shortcut)

$ ./a.out -ev -f John -l Doe "Book title" 2000
-- -e is processed, -v ignored

With a different program I have also experienced cases of a valid optional option being treated as a value for a positional argument, I will try to isolate that case later.

> I think that it may be useful to start "eating our own dog-food" and progressively make short, eiffeldoc and all the tool using that cluster, as I found it to be quite comfortable.

It's quite pleasant to use when coding, but the actual parsing sometimes works in unexpected ways and rejects option combinations which would be fine by the most usual Linux standards.
Letting all Liberty developers experience the shortcomings while using the tools may be useful as a way to accelerate the cluster's process of maturation, though :)

When executed with an ACE file as argument, eiffeldoc rejects any command line options except of -version and -verbose, making it impossible to provide -css, -js, -title and other presentation-related options. It doesn't seem to be possible to set them in the ACE file.

Some way to specify them should definitely be provided. I don't have a strong opinion if the right way to do so is allowing the command line options, adding new settings to the ACE file, or both.

(Related issue: Regarding -css and -js it would be preferable to include the /resources/eiffeldoc/eiffeldoc.(js|css) ones unless specified otherwise, because the unformatted HTML, as is currently produced by default, is ugly and useless. Default settings should provide reasonable results.)