Update workflow execution and recovery for dynamic output collections.

Galaxy workflow data flow before collections

* - * - * - * - * - *

Galaxy worfklow data flow after collections (iteration 1)

* - * - * \
           * - * - *
* - * - * /         \
                     * - * - *
* - * - * \         /
           * - * - *
* - * - * /

Galaxy worfklow data flow after this commit

              / * - * \
         * - *         * - *
        /     \ * - * /     \
       /                     \
      /                       \
     /        / * - * \        \
* - * -- * - *         * - * -- * - *
     \        \ * - * /        /
      \                       /
       \                     /
        \     / * - * \     /
         * - *         * - *
              \ * - * /