Consolidate ami regex tools

[remkop]

This is a follow-up item from discussion on #15:

@petermr I noticed there are two classes named AMIRegexTool and they both extend AbstractAMISearchTool. Which one should be the subcommand for ami? Or do you want both?

I picked org.contentmine.ami.tools.AMIRegexTool but it looks like that was the wrong one...

Note that org.contentmine.ami.plugins.regex.RegexPlugin is still available as a top-level command with a separate ami-regex launcher script. I can make that one the subcommand for ami if you want, but then what to do with org.contentmine.ami.tools.AMIRegexTool? (That one did not have a launcher script so perhaps you don't care too much about that one...)

Peter's reply:

What happened was a primitive pre-picocli command line which
supported something I called Plugins (they weren't actually Plugins as the
links were hardcoded but they were designed to be if and when I worked out
how! I even looked at OSGI at one stage).
AMIRegex is currently "broken" - i.e. it isn't linked in, but it should be.
It would be great to have the following:

• AMIRegex which is very useful for lots of things, such as identifiers.
  (There's a separate AMIIdentifier which is just a specialisation of regex.
• AMISpecies which uses style (...) to detect a possible species and
  then regex ([A-Z][a-z]+\s+[a-z]*) to pick up Tyrannosaurus rex . (The
  regex is more complex but ..). There's also more lookup logic - not just
  lexical.
• Gene, Sequence (biological), are also useful.
  and
  word frequencies also suffer from this mess.

If you look at org.contentmine.ami.plugins you can see these all had
pre-picocli commands (you can see why Picocli saved the project!!)

I have forgotten exactly how the commands linked in, but It should be
relatively easy to reconstruct a prototype. I started doing this but stuck
about halfway through (I think when I broke the leg). Somewhere in there I
have used a Bloom filter for rapid searching (I think it's still linked in).

But it may be that for general word searching and frequency it's better to
use Lucene/Solr and write results back into the tree.