[MRG] Remove --traverse-directory from commands & make default

[ctb]

Old behavior in 2.x and 3.x: when the user wants to load all signatures from under a directory, they must specify --traverse-directory to the command.

New behavior: if a directory is provided on the command line, it is automatically traversed for signatures (*.sig). -f still forces loading filenames that do not end with .sig.

This PR also modifies sourmash_args.load_dbs_sigs(...), .load_file_as_index(...), and load_file_as_signatures(...) to no longer take a traverseargument.

Fixes #836
Fixes #1061

• Is it mergeable?
• make test Did it pass the tests?
• make coverage Is the new code covered?
• Did it change the command-line interface? Only additions are allowed
  without a major version increment. Changing file formats also requires a
  major version number increment.
• Was a spellchecker run on the source code and documentation after
  changes were made?

[codecov]

Codecov Report

Merging #1178 into latest will increase coverage by 9.13%.
The diff coverage is 92.59%.

@@            Coverage Diff             @@
##           latest    #1178      +/-   ##
==========================================
+ Coverage   84.10%   93.24%   +9.13%     
==========================================
  Files          99       75      -24     
  Lines        9224     5906    -3318     
==========================================
- Hits         7758     5507    -2251     
+ Misses       1466      399    -1067     

Flag	Coverage Δ
#rusttests	?

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Impacted Files	Coverage Δ
sourmash/cli/categorize.py	100.00% <ø> (ø)
sourmash/cli/compare.py	100.00% <ø> (ø)
sourmash/cli/gather.py	100.00% <ø> (ø)
sourmash/cli/index.py	100.00% <ø> (ø)
sourmash/cli/lca/classify.py	100.00% <ø> (ø)
sourmash/cli/lca/index.py	100.00% <ø> (ø)
sourmash/cli/lca/summarize.py	100.00% <ø> (ø)
sourmash/cli/multigather.py	100.00% <ø> (ø)
sourmash/cli/search.py	100.00% <ø> (ø)
sourmash/lca/command_classify.py	88.75% <ø> (ø)
... and 29 more

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[bluegenes]

lgtm!