[DDC] update the module uris in metadata files to match the directory structure

[annagrin]

parent: dart-lang/webdev#1692

Proposed fix

make server paths follow directory structure:packages/<package_directory>/

Fix plan

DDC:
update the module uris in metadata files to match the scheme above, under a new debugger-module-uris flag

Note: is it needed? Check is the source map paths are absolute or relative when using build runner to compile the app.

[annagrin]

Update: looks like this is not necessary in build runner scenario, the new tests in dart-lang/webdev#1730 pass for build runner.