FAB-9698 fix TOC rendering in commands reference

also fixes defect in scripts/generateHelpDocs.sh caused
by change in default handling of config.yaml

also moves the files in 'wrappers' directory out
of the docs/source tree so that Sphinx does not
report them as missing from TOC. see FAB-9812

Change-Id: Ia3380b40a042fc8e6f3eaac4aaa087c959c6f1a3
Signed-off-by: Christopher Ferris <chrisfer@us.ibm.com>