One of the new features in EPiServer R2 version is the relocation of system folders. In previous versions they were stored in the same folder as the other site related files, but now they seem to be installed in Program Files by the new Installation Manager.
I fail to see the benefits of this. For safety and security reasons, software rarely have complete access to areas such as Program Files. To keep the development environment as similar to the deployment one as possible, the best way seems to be to set the VPP path to the classic location with all the other project files.
I read someone saying that this would act as a message to 3rd party vendors to keep their dirty fingers out of the cookie jar, but if someone is careless enough to mess with the EPiServer files in Util they will surely do so regardless of their location.

And then there is the issue with version control. Files such as web.config can cause trouble if they are kept under source control, as VPP paths are absolute and can differ from one developer to another. A suggestion here would be to break out the VPP paths from web.config and place them in another config file, just as with the connection strings.
Also, the name of the Program Files folder can change from one system language to another, which can add further to the confusion.
Feel free to illuminate me if you have any ideas on this.
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