Doc: Add .. program:: directives to new CLI tool help pages

[geographika]

This pull request adds .. program:: directives (see docs) as discussed in #14670.

This has the following advantages:

1. Previously, uses of :option: ... could link to a random page (specifically, the first page processed by Sphinx) rather than to the correct option on the program help page (see the example in Doc: :option: directives link to incorrect pages #14670 although this issue was widespread). These links are now fixed.
2. We can now link directly to an option from another page (see examples at b3059d1) using the syntax :option:`--overwrite <gdal_vector_buffer --overwrite> .
3. Adding the .. program:: directive highlights invalid options and broken option links on program pages. These issues have been addressed and are discussed below. Sphinx will also catch any new errors introduced on these pages.

Some program help pages used RST include files that linked to options not available for that program.

• doc/source/programs/gdal_options/warp_resampling.rst:
  removed the note linking to :option:--resolution and `:option:`--size because these options are not available in gdal raster update (they are available in gdal raster project)
• added doc/source/programs/gdal_options/input_layer_no_active_layer.rst for vector programs that use --input-layer but do not provide an --active-layer option, which was previously referenced in gdal_options/input_layer.rst
• added the missing --geometry-field option to gdal vector create
• removed the link to --add-alpha from gdal raster stack because this option is not available
• added the missing short-form option -r, which was linked to from gdal raster overview refresh and gdal raster overview add

I have not yet applied the .. program:: directive to the "traditional" pages. Most of these already include it, but I can review and add any missing directives in a separate PR.