Fix various YAML serialization issues

[speth]

Changes proposed in this pull request

• Fix serialization of changes to reaction/species flags with default values that are normally omitted, such as duplicate: true
• Add quotes when outputting strings that look like numbers, such as 123185 so they will be read in as strings rather than being implicitly converted to integers
• Remove initial indentation from multiline strings when serializing, to work around yaml-cpp's limited support of multiline strings.

If applicable, fill in the issue number this pull request is fixing

• Closes #1629
• Closes #1610
• Closes #1695

If applicable, provide an example illustrating new features this pull request is introducing

Checklist

• [x] The pull request includes a clear description of this code change
• [x] Commit messages have short titles and reference relevant issues
• [x] Build passes (scons build & scons test) and unit tests address code coverage
• [x] Style & formatting of contributed code follows contributing guidelines
• [x] The pull request is ready for review

[codecov[bot]]

Codecov Report

Attention: Patch coverage is 83.87097% with 10 lines in your changes missing coverage. Please review.

Project coverage is 73.04%. Comparing base (9210b08) to head (17e0ccf).

Files	Patch %	Lines
src/base/AnyMap.cpp	81.81%	2 Missing and 8 partials :warning:

Additional details and impacted files

```diff @@ Coverage Diff @@ ## main #1740 +/- ## ======================================= Coverage 73.03% 73.04% ======================================= Files 381 381 Lines 54132 54164 +32 Branches 9233 9240 +7 ======================================= + Hits 39534 39562 +28 + Misses 11635 11633 -2 - Partials 2963 2969 +6 ```

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