Parser rewrite

[multimeric]

User-Facing Changes

• Better distinction between description blocks and flags, allowing us to successfully parse flags of this form:

  --use_strict (enforce strict mode)
      type: bool  default: false
  --es5_readonly (activate correct semantics for inheriting readonliness)
      type: bool  default: true

• Support parsing multiple usage blocks, and add the UsageInstance class, which provides access to all these usage examples in the help. For example after parsing the text below, we would have 4 UsageInstances. The instances are provided on Command.usage:

  Usage:
  shell [options] -e string
  execute string in V8
  shell [options] file1 file2 ... filek
  run JavaScript scripts in file1, file2, ..., filek
  shell [options]
  shell [options] --shell [file1 file2 ... filek]
  run an interactive JavaScript shell

• Add flag and positional de-duplication, ensuring we don't have duplicate options in the final Command
• Add the max_length parameter to parse_help: If the input text has more than this many lines, no attempt will be made to parse the file (as it's too large, will likely take a long time, and there's probably an underlying problem if this has happened). In this case, an empty Command will be returned
• Enforce that Positionals always have at least 2-character names, in the parser
• Enforce that a Positional must have a description, in the parser

Internal Changes

• Rewrite of both the flag and usage parser
• Added more customizable indent tokens, meaning we no longer need the customIndentedBlock
• Refactor both the usage parser and the flag parser into subclasses of IndentParserMixin, which provides useful common parsing logic that relates to indentation
• Use MatchFirst instead of MatchLongest logic in most places in the parser. This should result in more consistent behaviour.
• Add typeHLA.js text, which is derived from the bwa-kit container.

Fixes

• Always strip out newlines from the WDL description