#201 tide-index and tide-search usage notes do not show all defaults

[Jeff Howbert]

In the command line usage notes for tide-index, the default parameter value is not specified for option:

--clip-nterm-methionine

For tide-search, the default parameter value is not specified for options:

--remove-precursor-peak
--concat
--use-neutral-loss-peaks

In addition, the example usage given for these tide-index options is uninformative:

--cterm-protein-mods-spec
--nterm-protein-mods-spec