Restore thesis.bcf from git commit if modified in workspace

This is a convenience to avoid having to remember to restore
this file after any broken compiles.

chertex.sh

@@ -191,6 +191,20 @@ if [[ $show_menu == "false" ]]; then
 
 	#### Special treatment for thesis
    if [[ $path_wd == "$path_thesis" && $jobname == "$dir_wd" ]]; then
+      # Restore thesis.bcf from latest commit if modified in workspace
+      # Background: any LaTeX run that finishes uncleanly (due to errors, etc.) leaves
+      # the  bcf file in an incomplete state. Since we have at least one plot in the thesis
+      # that reads the bcf file, this in turn causes the subsequent chertex compilation
+      # to fail. This mess could be automatically avoided if we pre-emptively check
+      # if thesis.bcf is listed in the output of `git status --short`, and if so `git restore` it.
+      # https://stackoverflow.com/a/25149786/1198249
+      if [[ `git status --porcelain | grep $jobname.bcf` ]]; then
+         msg "<thesis> -------------------------------"
+         msg "<thesis> Restoring thesis.bcf"
+         msg "<thesis> -------------------------------"
+         git -C $path_wd restore $jobname.bcf
+         simpledelay.sh 2
+      fi
       # Fetch external assets by reading any assets.external files in assets/ tree
       # NOTE: be careful NOT to leave empty lines in your assets.external files
       msg "<thesis> -------------------------------"