Install PEAR on Shared Host

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The manual gives all assurances of how easy this is, and it might be.
What I thought was strange was, this line:

"Pick a location to store your local copy of the remote code. "
ex: uses   C:\remote\pear

Later install packages, and they transparently, get uploaded as well.
Does this mean you have have PEAR installed in 2 different places on
your local machine?
C:\php\pear    would be standard location.

For remote installs would I use the  2nd location ?
Its a bit confusing, but I'm keeping my fingers crossed.

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