Specific methods for patch app configuration file scenarios

[shauns]

WHY are these changes introduced?

The current implementation of patchAppConfigurationFile is too broad, and we'll need something more specific if we want to switch out for a format preserving patcher.

WHAT is this pull request doing?

This PR introduces three new, more intuitive functions for modifying app configuration:

1. setAppConfigValue - Sets a single value in the app configuration using a dotted path notation
2. unsetAppConfigValue - Removes a value from the app configuration
3. setManyAppConfigValues - Sets multiple values at once in the app configuration

The original patchAppConfigurationFile function is now marked as internal, and all existing usages have been updated to use the new functions. This provides a more declarative API for modifying configuration values.

How to test your changes?

1. Run the test suite to verify all tests pass
2. Try using the CLI to modify app configuration values (e.g., dev command that updates URLs)
3. Verify that the TOML file is correctly updated with the expected values

Measuring impact

How do we know this change was effective? Please choose one:

• n/a - this doesn't need measurement, e.g. a linting rule or a bug-fix

Checklist

• I've considered possible cross-platform impacts (Mac, Linux, Windows)
• I've considered possible documentation changes

[shauns]

• Specific methods for patch app configuration file scenarios #5641 : 2 dependent PRs (#5642 , #5677 ) 👈 (View in Graphite)
• main

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[github-actions]

Coverage report

St.❔	Category	Percentage	Covered / Total
🟡	Statements	76.73% (+0.06% 🔼)	9501/12383
🟡	Branches	71.77% (+0.01% 🔼)	4657/6489
🟡	Functions	76.51% (+0.06% 🔼)	2462/3218
🟡	Lines	77.27% (+0.06% 🔼)	8986/11630

Show files with reduced coverage 🔻

St.❔	File	Statements	Branches	Functions	Lines
🟢	... / context.ts	78.26% (-0.37% 🔻)	65.67%	79.17%	80.81% (-0.38% 🔻)
🟢	... / patch-app-configuration-file.ts	100%	62.5% (-37.5% 🔻)	100%	100%

Test suite run success

2211 tests passing in 961 suites.

Report generated by 🧪jest coverage report action from 953e0ef

[github-actions]

We detected some changes at packages/*/src and there are no updates in the .changeset.
If the changes are user-facing, run "pnpm changeset add" to track your changes and include them in the next release CHANGELOG.