Remove unnecessary executable permissions from example and test scripts

[Esteban82]

Assisted-by: Claude Sonnet 5 (High effort)

Removed the executable permission from example and test .sh scripts under doc/ and test/.
Updated the code-validator.yml CI checker to reflect this new policy.

Closes#9048

[seisman]

I don't think these scripts need executable permissions. They can be run via bash xxx.sh.

$ find . -name "*.sh" ! -path "./doc/*" ! -path "./test/*" \
! -path "./share/tools/gmt_functions.sh"
./ci/config-gmt-windows.sh
./ci/config-gmt-unix.sh
./ci/download-coastlines.sh
./ci/install-dependencies-linux.sh
./ci/install-dependencies-macos.sh
./ci/simple-gmt-tests.sh
./ci/deploy-gh-pages.sh
./ci/build-gmt.sh
./ci/install-dependencies-windows.sh
./admin/src_replace_word.sh
./admin/src_convention_check.sh
./admin/build-scientific-colors-cpt.sh
./admin/build-macos-external-list.sh
./admin/copyright_year.sh
./admin/list_known_failures.sh
./admin/remote_files_used.sh
./admin/run_cppcheck.sh
./admin/git_release_history.sh
./admin/image_optimize.sh
./admin/gs_check.sh
./admin/build-macos-cmake-cache.sh
./admin/gmt_make_pattern_include.sh
./admin/build-cmocean-cpt.sh
./admin/examine-failure-log.sh
./admin/build-release.sh
./admin/place-release.sh
./share/tools/gmt_links.sh
./share/tools/gmt_prepmex.sh
./share/tools/gmt_uninstall.sh
./share/tools/christmas-cube.sh
./src/gsfml/fz_funcs.sh
./src/gmt_make_PSL_strings.sh
./src/gmt_make_enum_dicts.sh
./src/gmt_make_module_purpose.sh
./src/spotter/spotter.sh
./src/shelltest.sh
./src/windbarbs/test/grdbarb_example.sh
./src/windbarbs/test/psbarb_example.sh
./src/mgd77/make_new_dst.sh
./src/mgd77/reformat_kyoto_dst.sh
./src/mgd77/mgd77netcdfhelper.sh
./src/mgd77/mgd77_codes.sh
./src/x2sys/test_x2sys.sh
./src/gmt_shell_functions.sh

[seisman]

gmt_functions.sh is expected to be used like source gmt_functions.sh, so it also doesn't need executable permission.

[Esteban82]

Fixed now. No more exceptions, no *.sh should be executable.

[seisman]

The Tests workflow fails and needs to be fixed. it can be done in a separate PR because this PR already contains too many changed files.

[Esteban82]

The Tests workflow fails and needs to be fixed. it can be done in a separate PR because this PR already contains too many changed files.

They are failing because of this PR, right?

[seisman]

I think we need to update

gmt/test/gmtest.in

Line 309 in 6312737

. "${local_script}"

to

bash "${local_script}"

[Esteban82]

It sounds fine. I will do make another PR for this.

[joa-quim]

I don’t understand why is needed this to change all these files. If the solution is to call them prefixed with bash it doesn’t matter if they have the executable mode or not.

[seisman]

As I understand it, scripts created under Windows do not have executable permissions by default. Consequently, we may encounter inconsistent executable permissions across our scripts in the future.