Fix some places where Debug/Release was treated as a binary switch.

Makes similar changes to Windows and Linux to simplify adding profile
support to those platforms in the future. This means `--profile` builds
will fail on Linux and Windows for now, but that's fine since they
aren't actually supported, and unlike `--release` don't provide useful
functionality at the native code level.

Also fixes 'stopApp' always using Debug on macOS, to avoid showing an
error when running Profile (or Release).

Fixes #33203

Slight cleanup of file locations in flutter_tools
to make it easier to see which files are responsible
for data reporting.

- Adds desktop projects to ApplicationPackageStore
- Plumbs target overrides through the macOS build

Enables the CocoaPods-based plugin workflow for macOS. This allows a
macOS project to automatically fetch and add native plugin
implementations via CocoaPods for anything in pubspec.yaml, as is done
on iOS.

This is necesasry to integrate CocoaPods, since CocoaPods operates
primarily on the workspace rather than the project.

- Removes SYMROOT from the Generated.xcconfig. Having it causes current
  versions of Xcode to switch the project's build output to "Legacy",
  which causes anything not overridden to use a project-relative build
  directory instead of a shared directory in DerivedData, breaking
  anything with subprojects that it depends on.
  This means that `flutter run` and builds from Xcode will use
  completely different build directories, but that each should be
  internally consistent.
- Moves the FlutterMacOS.framework to $SRCROOT/Flutter. This is
  consistent with the approach we're moving to for all desktop
  platforms, and avoids issues finding it now that SYMROOT doesn't match
  for the two different build modes.

Fixes #32494