* When cleaning the stage root, only remove directories that appear
to be used for staging Spack packages. Previously Spack was clearing
all directories in the stage root, which could remove content not
related to Spack if the user chose a staging root which contains
files/directories not managed by Spack.
* The documentation is updated with warnings about choosing a stage
directory that is only managed by Spack (although generally the
check added in this PR for "spack clean" should avoid removing
content that was not created by Spack)
* The default stage directory (in config.yaml) is now
$tempdir/$user/spack-stage and the logic is updated to omit the
$user portion of this path if $tempdir already contains a $user
directory.
* When creating stage root assign user read/write permissions to all
directories in the path under $user. Previously Spack was assigning
the permissions of the first existing parent directory
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