Closes #3587.

[pod repo push] Discover and push JSON specs while pushing from a directory

[Resolver] Move side-effect of storing head pods from #specs_by_target

Closes #3494

Ref #3494

Projects opened via pod try are now editable
Closes https://github.com/CocoaPods/cocoapods-try/issues/31

This reverts commit 28c5c44d.

[Config] Add #with_changes

[Downloader] Actually allow skipping the cache entirely

[PodTargetInstaller] Don't generate an umbrella header when a custom mod...

[Installer] Copy Podfile.lock to Manifest.lock rather than using #wri…

[Cache] Fix the cache to handle re-downloads properly

Just remove write permissions from files, so executables are unaffected

[Installer] Check for regular file on lock

[UI] Disambiguate gem and pod updates

This patch check if a file is a regular file instead of checking if the file is a
directory.

It fixes a crash when the file being analysed is a broken symbolic link.

[Sandbox::FileAccessor] Add missing `.cc` extension for C++ to `SOURCE_FILE_EXTENSIONS`.

[TargetIntegrator] Only embed application and unit test bundle targets