add handling of a .skip_lint file

that allows to list linters to be skipped. a skip file in the repo root
and in the tool dir are allowed (and joined)

planemo_ci_actions.sh

@@ -110,10 +110,12 @@ fi
 # - check if each tool is in a repo (i.e. if `.shed.yml` is present)
 if [ "$MODE" == "lint" ]; then
   lint_fail=false
+  touch .lint_skip
   mapfile -t REPO_ARRAY < repository_list.txt
   for DIR in "${REPO_ARRAY[@]}"; do
     if [ "$WORKFLOWS" != "true" ]; then
-      (planemo shed_lint --tools --ensure_metadata --urls --report_level "$REPORT_LEVEL" --fail_level "$FAIL_LEVEL" --recursive "$DIR" "${ADDITIONAL_PLANEMO_OPTIONS[@]}" | tee -a lint_report.txt) || lint_fail=true
+      cat .lint_skip >> "$DIR"/.tt_skip
+      (planemo shed_lint --tools --ensure_metadata --urls --skip_file "$DIR"/.tt_skip --report_level "$REPORT_LEVEL" --fail_level "$FAIL_LEVEL" --recursive "$DIR" "${ADDITIONAL_PLANEMO_OPTIONS[@]}" | tee -a lint_report.txt) || lint_fail=true
     else
       (planemo workflow_lint --report_level "$REPORT_LEVEL" --fail_level "$FAIL_LEVEL" "$DIR" "${ADDITIONAL_PLANEMO_OPTIONS[@]}" | tee -a lint_report.txt) || lint_fail=true
     fi