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I know most programs won't notice the difference, but is it true for e.g. virtualization software like VMware?

I'll give you an example:

  1. Let's say my virtual machines are in C:\_VM\
  2. My C: space runs low.
  3. I start Windows 7 in safe-mode.
  4. Change the name of the folder (to e.g. C:\_VM_tmp\).
  5. Create new partition and mount it to C:\_VM\.
  6. Copy contents of C:\_VM_tmp\ to C:\_VM\.
  7. Restart.

Would all just work or would I be in trouble?

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up vote 4 down vote accepted

The application in general would not care, unless it tries hard to. Mounting a drive to a directory is transparent to the application, i.e., the app is oblivious to that fact.

Vmplayer or vmware workstation does not.

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Your programmes shouldn't care where ever your files are. Unless, that is, Windows 7's way of mounting partitions is vastly different from Linux's. I would go ahead with it if I were you.

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