Setup and add-3d can report success after a failed write #20

Found during #17 review.

• commands/setup/changes.py (~124-126, ~225-227) and setup/command.py (~224-227): environment-variable and pin write failures can be treated as unchanged state while setup continues and reports success.
• commands/setup/changes.py (~187-190): library-table additions use only the primary symbol-library directory even when several libraries are selected.
• commands/add_3d/command.py (~99, ~132, ~258): metadata write results are ignored.
• utils/metadata writers truncate the file before writing; use write_atomically so a failed write cannot leave it empty.