Steps to reproduce:
1. Open attached project
2. In Packages/ set manifest.json to read-only
3. In the project folder edit build-exe.bat file and set the path to your unity.exe file
4. Start the build-exe.bat file
(Optional)
5. Check Editor.log

Expected: Unity can build a project from read-only source files, e.g. a Perforce checkout, without needing to check out and make modifications.
Actual: Unity build fails with error*

Reproduced in: b8, 2018.2.0b8, 2018.2.0f2, b6, 2018.3.0a4
Not reproduced in: 2017.1.4p2, 2017.2.3p2, 2017.3.2p2, 2017.4.7f1, 2018.1.8f1, 2018.2.0a1, 2018.2.0b7
*Error:
[Package Manager] A change to the read-only file [E:/Downloads/case_1058480-simple-app/Packages/manifest.json] is required to continue.

Resolution:
This was done by design. It will happen in cases where the project is used with a different Unity version and an upgrade is required. Not performing the upgrade would result in a different result, and likely introduce errors (compilation failures due to missing packages for instance).