Fix JPM repository 'Update All' action

`TreeSet` requires its elements to be Comparable, causing an exception
in this code path.  Change to a List instead because order should be
guaranteed by the `SortedSet` returned by `Index.getVersions()`.

Signed-off-by: Sean Bright <sean@malleable.com>
Resolve ConcurrentModificationException on JPM update

Updating the index may involve deleting elements from the underlying
`Map` which we can't do safely without copying the keyset first.

Signed-off-by: Sean Bright <sean@malleable.com>