zephyr: Generated linker scripts break when ZEPHYR_BASE and ZEPHYR_MODULES share structure that contains symlinks

Describe the bug My zephyr workspace consists of symlinks to read-only copies of modules which exist in a programmatically managed filesystem. The filesystem looks something like this.

-/store
\-- zephyr-base
\-- hal-nxp
\-- cmsis
\-- zcbor
- /workspace
-- zephyr -> /store/zephyr-base
-- modules/hal/nxp -> /store/hal-nxp
-- modules/hal/cmsis -> /store/cmsis

This command builds successfully:

source /store/zephyr/zephyr-env.sh

cmake $ZEPHYR_BASE/samples/hello_world \
-Bbuild -DBOARD=frdm_k64f \
-DZEPHYR_MODULES=/store/hal-nxp;/store/cmsis
 
make -Cbuild

This command fails to build:

source /workspace/zephyr/zephyr-env.sh

cmake $ZEPHYR_BASE/samples/hello_world \
-Bbuild -DBOARD=frdm_k64f \
-DZEPHYR_MODULES=/workspace/modules/hal/nxp;/workspace/modules/hal/cmsis 

make -Cbuild

The reason is because the generated linker scripts in build/zephyr/include/generated/ use relative paths to $ZEPHYR_BASE. When the build is running it thinks its running from wherever it really is in the filesystem, i.e. /store/zephyr instead of ./workspace/zephyr. The linker generates an include that looks like

/* Sort key: "default" */#include "../../../modules/hal/nxp/mcux/quick_access_code.ld"

But starting from /store/zephyr/ there is no …/…/…/modules. If any of the “…/” are symlinks at configure time the build will fail.

If these files would embed absolute paths instead the symlinks would be resolved correctly at configure and build time. Is there any reason to prefer relative paths over absolute paths?