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 https://github.com/glotzerlab/signac-docs/pull/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:

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

[codecov[bot]]

Codecov Report

All modified and coverable lines are covered by tests :white_check_mark:

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

Additional details and impacted files

```diff @@ Coverage Diff @@ ## main #970 +/- ## ========================================== + 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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