Make newly-added add-source deps override previously installed versions.

Fixes #1197.

This patch is a bit large because it includes several related changes:

1) Remove `installUseSandbox` from `InstallFlags` and pass `useSandbox` as an additional argument instead.

2) Instead of calling `reinstallAddSourceDeps` from `installAction`, always pass `SandboxPackageInfo` to `install`.

3) Set the timestamps of newly-added add-source deps to 0 in the timestamp file.

4) Move the timestamp file update to `postInstallActions` from `withModifiedDeps`. This way, the timestamps are updated even when the user runs `install --only-dependencies` or `install some-add-source-dep-package-id`.