fixed several isses in vdb_tool

[kmuseth]

Fixed some corner cases in vdb_tool, some uncovered by Astra in extreme mode, and others resulting from tests on the Thingi10K data set:

• Preserve rebuilt CSG results when replacing input grids.
• Return a failing exit status after action errors and stop immediately on
  control-flow errors instead of entering invalid scopes.
• Preserve input grids after failed VDB/NanoVDB writes and avoid changing
  the grid stack or names when voxel-kernel variable validation fails.
• Preserve modulo expressions and loop counters in configuration files.
  Inline comments now use '#'; '%' still supports full-line comments.
• Reject truncated or malformed PLY data instead of hanging or reading
  incomplete records.
• Support descending loops and reject zero or non-progressing steps.
• Keep binary stdout separate from diagnostic logs in both logging modes.