Fix parsing of $not expression on command line

[cbkerr]

Description

• fixes bug
• adds test to test_shell.py
• I do not fix the testing code in test_find_command_line_interface.py that does not properly test the code path but I left a todo for now.

Motivation and Context

The $not expression was broken on the command line. I noticed this while working on glotzerlab/signac-docs#199

signac was inserting sp. prefixes before the operator

$ signac find '{"$not": {"a": 1}}'
Error: "Invalid operator placement 'sp.$not.a'."

The function filterparse._add_prefix does the inserting, which later triggered an error in _search_indexer._find_expression. This code path wasn't tested.

Checklist:

• I am familiar with the Contributing Guidelines.
• I agree with the terms of the Contributor Agreement.
• My name is on the list of contributors.
• The changes introduced by this pull request are covered by existing or newly introduced tests.
• The package documentation and framework documentation in signac-docs are up to date with these changes.
• I have updated the changelog and added any related issue and pull request numbers for future reference.

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Comparison is base (f9df893) 85.65% compared to head (b4b0cc2) 85.71%.

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #970      +/-   ##
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+ Coverage   85.65%   85.71%   +0.06%     
==========================================
  Files          20       20              
  Lines        3464     3466       +2     
  Branches      759      760       +1     
==========================================
+ Hits         2967     2971       +4     
+ Misses        338      337       -1     
+ Partials      159      158       -1     

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[bdice]

I'd like to see test_shell avoid importing from test_find_command_line_interface, but I won't block this PR on that.