Save URI returned only from FileEntry::getRemainingUris()

The currently used URIs are inserted back into remaining URI list in
FileEntry::putBackRequest(), which overlaps to some of the URIs in
spentUris_. If we save spent URIs, each time save is performed, the
number of URIs are increased due to this overlap. This change fixes
this bug.
Save options directly specified for download in --save-session

This change makes --save-session save only options specified for
download, more specifically, options in command-line, -i file and via
RPC. The other options from conf file and default values are not
saved.  This will drastically decrease the size of session file.