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In hello world sample, do following steps, may get compile error.

Step1: vim prj.conf, add:
CONFIG_MBEDTLS=y
CONFIG_MBEDTLS_BUILTIN=y

Step2: vim src/main.c, add:
#include <mbedtls/sha256.h> above the main function.

Step3:
mkdir -p build/nrf51_pca10028 && cd build/nrf51_pca10028
cmake -DBOARD=nrf51_pca10028 ./ ../../
make -j4

Step4: Output with error:

/home/username/project/zephyr/samples/hello_world/src/main.c:10:28: fatal error: mbedtls/sha256.h: No such file or directory
#include <mbedtls/sha256.h>
compilation terminated.
CMakeFiles/app.dir/build.make:302: recipe for target 'CMakeFiles/app.dir/src/main.c.obj' failed
make[2]: *** [CMakeFiles/app.dir/src/main.c.obj] Error 1
CMakeFiles/Makefile2:259: recipe for target 'CMakeFiles/app.dir/all' failed
make[1]: *** [CMakeFiles/app.dir/all] Error 2
make[1]: *** Waiting for unfinished jobs....

This error message also shown up when using file system, when have head file fs.h included (#include <fs.h> ).

In hello world sample, do following steps, get compile error.

Step1: vim prj.conf, add:
CONFIG_FLASH=y
CONFIG_FILE_SYSTEM=y
CONFIG_FILE_SYSTEM_NFFS=y

Step2: vim src/main.c, add:
#include <fs.h> above the main function.

Step3:
mkdir -p build/frdm_k64f && cd build/frdm_k64f
cmake -DBOARD=frdm_k64f ./ ../../
make -j4

Step4: Output with error:

In file included from /home/username/project/zephyr/include/fs/fs_interface.h:47:0,
from /home/username/project/zephyr/include/fs.h:11,
from /home/username/project/zephyr/samples/hello_world/src/main.c:10:
/home/trylong/project/zephyr/include/fs/nffs_fs.h:11:23: fatal error: nffs/nffs.h: No such file or directory
#include <nffs/nffs.h>
compilation terminated.
CMakeFiles/app.dir/build.make:302: recipe for target 'CMakeFiles/app.dir/src/main.c.obj' failed
make[2]: *** [CMakeFiles/app.dir/src/main.c.obj] Error 1
CMakeFiles/Makefile2:259: recipe for target 'CMakeFiles/app.dir/all' failed
make[1]: *** [CMakeFiles/app.dir/all] Error 2
make[1]: *** Waiting for unfinished jobs....

Same error when use FAT file system.

You are discovering a known, but undocumented usability issue.

This is now tracked here: #5351

Look at how other samples are using mbedTLS and fs. They are doing

target_link_libraries(app mbedTLS)

PS: I didn't investigate the FS issue but I assume it is the same as mbedtls.