Fix broken links #537

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9 warnings

The following actions uses node12 which is deprecated and will be forced to run on node16: actions/checkout@v2. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/

file=R/bbt_continue.R,line=140,col=8,[indentation_linter] Indentation should be 6 spaces but is 8 spaces.

file=R/bbt_continue.R,line=142,col=8,[indentation_linter] Indentation should be 6 spaces but is 8 spaces.

file=R/bbt_delete_temp_files.R,line=54,col=4,[indentation_linter] Indentation should be 6 spaces but is 4 spaces.

file=R/bbt_delete_temp_files.R,line=59,col=4,[indentation_linter] Indentation should be 6 spaces but is 4 spaces.

file=R/bbt_run_from_model.R,line=133,col=4,[indentation_linter] Indentation should be 6 spaces but is 4 spaces.

file=R/check_beast2_pkgs.R,line=26,col=17,[object_usage_linter] no visible global function definition for 'get_default_beast2_bin_path'

file=R/check_beast2_pkgs.R,line=30,col=4,[indentation_linter] Indentation should be 6 spaces but is 4 spaces.

file=tests/testthat/test-bbt_run_from_model.R,line=221,col=0,[indentation_linter] Indentation should be 2 spaces but is 0 spaces.