Change nestling structure

Fit to the same including structure as the included polygons yaml in main input of prepare_schism

Author: qiangshu

examples/bctides/bctides.in.2d.yaml

@@ -1,4 +1,5 @@
-bctides.2d.in:
+bctides:
+  - name: bctides.2d.in
     mode: barotropic # option barotropic or baroclinic
     temperature_salinity_computation: false # true/false, it is used only when mode is barotropic,
                                             # if true then temperature and salinity is requried on 

examples/bctides/bctides.in.3d.tide.yaml

@@ -2,7 +2,8 @@
 # If so we should accommodate that here.
 # Don't forget that time_history_nc is an option
 # Let's be rigorous about velocity/flow and make sure exactly zero (tidal) or one is specified 
-bctides.tide.sed.in.3d:
+bctides:
+  - name: bctides.sed.in.3d
     modules:
       - name: GEN
         num_tracers: 1

examples/bctides/bctides.in.3d.yaml

@@ -1,4 +1,5 @@
-bctides.3d.in:
+bctides:    
+  - name: bctides.3d.in
     date: 2011-01-28
     mode: baroclinic # option barotropic or baroclinic
     temperature_salinity_computation: true # true/false, it is used only when mode is barotropic,

examples/bctides/bctides.in.sed.3d.yaml

@@ -1,4 +1,5 @@
-bctides.sed.3d.in:
+bctides:
+  - name: bctides.sed.3d.in
     modules:
       - name: SED
         num_tracers: 3