Repro steps:
1. Make a NEW project in Unity 2018.1
2. Enable Collaborate
3. Add a package (for example, Post Processing Stack)
4. Commit to Unity 2018.1
5. Delete the project locally
6. Open Unity 2018.2.0f2 and download the project from the cloud.
Notice:
- no warnings that you're opening the project with a newer Unity version
- errors in regards to missing packages
- Package Manager window cannot be opened
- manifest.json only has that one Post Processing package in it (compared to the large number of required packages for Unity 2018.2)

Workaround: Download the project with Unity 2018.1 and save it locally and then proceed to upgrade it to Unity 2018.2
Second workaround: Use Help -> Reset Packages to Default

Regressed version: Unity 2018.2.0b8