From the Mouseplanet weekly Disneyland Update:
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Less exciting from a visual perspective, but still interesting to those following the construction process, is a building permit Disney filed the same day for the second phase of the project. This permit includes the construction of a 12,000 sq. ft. subterranean marina with pump and power stations; a 5,573-linear-foot retaining wall; four bridge/trestle structures; and three tunnels.
Taking these individually, here's our best guess about what Disney is building:
Marina – this is likely a storage area for the watercraft (barges and Crocodile) used for Fantasmic. The quarter-acre structure probably won't actually be "underground," but built into the redesigned berm around Disneyland.
Retaining wall – this is likely the redesigned berm. The permit also calls for more than 900 linear feet of landscaped retaining wall.
Bridges, trestles and tunnels – based on the permit, we expect the new train route to cross over water in one place (likely at the inlet to the new marina structure), and to cross over walkways in three additional places. Those three walkways would likely be the "tunnels" listed on the permit, similar to the entrance to Toontown. The permit specifies two bridges and two trestles; these terms refer to the type of construction.
This permit just covers one small phase of the construction, so there's nothing too exciting here. Still, it's fun to keep tabs on the work. For now, enjoy the view of the construction scene."