Fixes time mismatch issues with prepare when using symlinks

[tzraikov]

Steps to reproduce:

1. Clone nativescript and create npm link in tns-core-modules
2. Create a new {N} project
3. Run the project
4. Remove tns-core-modules folder from the project modules path
5. Execute npm link tns-core-modules
6. Expected: the project should be prepared and build. Actual: both steps are skipped.

Merge after:
telerik/mobile-cli-lib#834