Fix handling of xtime variable in mpas_to_xdmf

[xylar]

This PR also fixes indexing in xdmf jinja template.

[xylar]

Testing

I was able to run this successfully with the following 3-month time series of sea-surface height:

cd /lcrc/group/e3sm/ac.xylar/scratch/chrys/20250812.GMPAS-JRA1p5-DIB-PISMF-SIS.TL319_SOwISC12to30E3r4_ais4to20.coupler_budget.chrysalis/run
mpas_to_xdmf -m 20250812.GMPAS-JRA1p5-DIB-PISMF-SIS.TL319_SOwISC12to30E3r4_ais4to20.coupler_budget.chrysalis.mpaso.rst.0001-04-01_00000.nc -t 20250812.GMPAS-JRA1p5-DIB-PISMF-SIS.TL319_SOwISC12to30E3r4_ais4to20.coupler_budget.chrysalis.mpaso.hist.am.timeSeriesStatsMonthly.* -v timeMonthly_avg_ssh -x xtime_startMonthly -o xdmf_ssh

Without these fixes, I first saw an error:

  File "/gpfs/fs1/home/ac.xylar/mpas_work/MPAS-Tools/fix-paraview-extractor/conda_package/mpas_tools/viz/mpas_to_xdmf/io.py", line 96, in _load_dataset
    _set_time(ds=ds, xtime_var=xtime_var)
    ~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/gpfs/fs1/home/ac.xylar/mpas_work/MPAS-Tools/fix-paraview-extractor/conda_package/mpas_tools/viz/mpas_to_xdmf/time.py", line 23, in _set_time
    raise ValueError(
        f"xtime variable '{xtime_var}' not found in dataset."
    )
ValueError: xtime variable 'xtime_startMonthly' not found in dataset.
(mpas_tools_dev) [ac.xasay-davis@chrlogin1 run]$ mpas_to_xdmf -m 20250

and then I saw an XDMF file that just repeated time index 0:

<?xml version="1.0" ?>
<Xdmf Version="3.0" xmlns:xi="http://www.w3.org/2001/XInclude">
  <Domain>
    <Grid Name="TimeSeries" GridType="Collection" CollectionType="Temporal">
      
      
      
      <Grid Name="Step0" GridType="Uniform">
        <Time Value="0.0"/>
        <Topology TopologyType="Polygon" NumberOfElements="807754" NodesPerElement="8">
          <DataItem Format="HDF" Dimensions="807754 8">fieldsOnCells.h5:/Cells</DataItem>
        </Topology>
        <Geometry GeometryType="XYZ">
          <DataItem Format="HDF" Dimensions="1631441 3">fieldsOnCells.h5:/Points</DataItem>
        </Geometry>
        
        
        <Attribute Name="timeMonthly_avg_ssh" AttributeType="Scalar" Center="Cell">
          <DataItem Format="HDF" Dimensions="807754">fieldsOnCells.h5:/timeMonthly_avg_ssh_t0</DataItem>
        </Attribute>
        
        
      </Grid>
      
      
      <Grid Name="Step0" GridType="Uniform">
        <Time Value="2676000.0"/>
        <Topology TopologyType="Polygon" NumberOfElements="807754" NodesPerElement="8">
          <DataItem Format="HDF" Dimensions="807754 8">fieldsOnCells.h5:/Cells</DataItem>
        </Topology>
        <Geometry GeometryType="XYZ">
          <DataItem Format="HDF" Dimensions="1631441 3">fieldsOnCells.h5:/Points</DataItem>
        </Geometry>
        
        
        <Attribute Name="timeMonthly_avg_ssh" AttributeType="Scalar" Center="Cell">
          <DataItem Format="HDF" Dimensions="807754">fieldsOnCells.h5:/timeMonthly_avg_ssh_t0</DataItem>
        </Attribute>
        
        
      </Grid>
      
      
      <Grid Name="Step0" GridType="Uniform">
        <Time Value="5095200.0"/>
        <Topology TopologyType="Polygon" NumberOfElements="807754" NodesPerElement="8">
          <DataItem Format="HDF" Dimensions="807754 8">fieldsOnCells.h5:/Cells</DataItem>
        </Topology>
        <Geometry GeometryType="XYZ">
          <DataItem Format="HDF" Dimensions="1631441 3">fieldsOnCells.h5:/Points</DataItem>
        </Geometry>
        
        
        <Attribute Name="timeMonthly_avg_ssh" AttributeType="Scalar" Center="Cell">
          <DataItem Format="HDF" Dimensions="807754">fieldsOnCells.h5:/timeMonthly_avg_ssh_t0</DataItem>
        </Attribute>
        
        
      </Grid>
      
      
      
    </Grid>
  </Domain>
</Xdmf>