Add caching section to Parrot manual.

Fixes #327.
Add option --recheck-file-creation.

To handle NFS semantics, this option tells makeflow not to fail
if a file from a succesful job is not immeditely available. Makeflow
retries for the file before failing.
Merge remote-tracking branch 'ccl/pull/646/head'

* ccl/pull/646/head:
  Add caching section to Parrot manual.
Allow user to set tries/wait time
Merge pull request #647 from btovar/patience_nfs

Add option --recheck-file-creation.
Added all: target so default make does nothing with apps
Merge pull request #649 from nhazekam/apps_make

Added all: target so default make does nothing with apps
Simplifies recheck option for NFS.

I don't know what I was thinking. Simplifying from three command line
switches to one. Now use:

--wait-for-files-upto=<n>

to wait upto n seconds for files to appear at the filesystem running
makeflow.
Merge branch 'master' of github.com:cooperative-computing-lab/cctools