Compiler and linker flags can be altered on different levels in the project. Options added to the csolution.yml files can be included in all sub projects. Options added to the cproject.yml files are project-specific.

For csolution.yml, options are specified under build-types, like this:

build-types:
- type: MyType
  compiler: IAR
  misc:
   - C:
     - "‑‑newOption"
   - Link:
     - "‑‑alsoNewOption"

A misc section can also be added to the project entry in the cproject.yml file for project-specific options, or as conditional arguments for specific compilers and contexts under the setups section, like this:

setups:
    - setup: IAR_Setup
      for-compiler: IAR
      misc:
        - CPP:
          - "‑‑c++"
      linker:
          - script: linker.icf
      define:
          - test: 12

For more information, see the official CMSIS-Toolbox documentation.