Change root criteria in rprojroot::find_root

Add rprojroot::has_file(".git") as an alternative root criterion to
handle linked git working trees created by `git worktree add` in
rprojroot::find_root.

analyses/long-format-table-utils/annotator/annotator-cli.R

@@ -24,7 +24,7 @@
 
 
 # source annotator-api.R to get the annotate_long_format_table function --------
-# Detect the ".git" folder -- this will in the project root directory. Use
+# Detect the ".git" folder -- this will be in the project root directory. Use
 # this as the root directory to ensure proper execution, no matter where it is
 # called from.
 #
@@ -33,10 +33,22 @@
 #
 # root_dir is the absolute path of OpenPedCan-analysis
 #
-# Adapted from the oncoprint-landscape module.
+# Adapted from the oncoprint-landscape module
+#
+# rprojroot::has_file(".git/index") returns a rprojroot::root_criterion, and
+# main git working tree, created by git clone and git init, has the .git/index
+# file
+#
+# rprojroot::has_file(".git") returns a rprojroot::root_criterion, and linked
+# git working tree, created by git worktree add, has the .git file
+#
+# "Root criteria can be combined with the | operator. The result is a
+# composite root criterion that requires either of the original criteria to
+# match." -- help("root_criterion", "rprojroot") rprojroot_1.3-2
 tryCatch(
   {
-    root_dir <- rprojroot::find_root(rprojroot::has_file(".git/index"))
+    root_dir <- rprojroot::find_root(
+      rprojroot::has_file(".git/index") | rprojroot::has_file(".git"))
   },
   error = function(err_cond) {
     # adapted from http://adv-r.had.co.nz/Exceptions-Debugging.html