Two-stage compile has 0 file reported at the second stage

When two-stage compilation is enabled, the build failed for LFRic gungho at the moment with an error `/scratch/hc46/hc46_gitlab/lfric_fab/gungho_model-mpif90-ifort/build_output/_prebuild/physics_mappings_alg_mod.cb6a16b9a.o` not found at link stage.

It is observed that the following messges are logged during the compile_fortran step:

`Starting two-stage compile: mod files, multiple passes`
...
`Finalising two-stage compile: object files, single pass`
...
`stage 2 compiled 0 files`

There are actually a number of compiling commands being executed between `Finalising two-stage compile: object files, single pass` and `stage 2 compiled 0 files`. So I am wondering whether there is a bug in updating the build tree.

The build log is here: https://git.nci.org.au/bom/ngm/lfric/lfric_atm-fab/-/jobs/80826