The current assets.external implementation cannot handle empty lines.

Added a comment to warn about that.

chertex.sh

@@ -35,8 +35,8 @@ Rfiletype="R"
 TeXfiletype="tex"
 tikzfiles="*.tikz"
 Rnwfiles="*.Rnw"
-auxfiles="*.acn *.acr *.alg *.aux *.bbl *.bcf *.blg *.dep *.dpth *.fdb* *.figlist *.fls *.glg 
-*.glo *.gls *.lof *.log *.lor *.los *.lot *.out *.lox *.makefile *.map *.out *.run* *.slg *.slo 
+auxfiles="*.acn *.acr *.alg *.aux *.bbl *.bcf *.blg *.dep *.dpth *.fdb* *.figlist *.fls *.glg
+*.glo *.gls *.lof *.log *.lor *.los *.lot *.out *.lox *.makefile *.map *.out *.run* *.slg *.slo
 *.sls *.tdo *.toc *.xdy"
 
 
@@ -89,12 +89,13 @@ if [ $# -eq 1 ]; then
 	#### Special treatment for thesis
    if [[ ${PWD} ==  "/media/bay/taha/chepec/thesis" && $jobname == "thesis" ]]; then
       # Fetch external assets by reading any assets.external files in assets/ tree
+      # NOTE: be careful NOT to leave empty lines in your assets.external files
       echo "<thesis> -------------------------------"
       echo "<thesis> Getting external assets"
       echo "<thesis> -------------------------------"
-		# summary of operations in this if-clause:
+		  # summary of operations in this if-clause:
       # trawl the assets/ subdirectories looking for a file "external.assets", if found,
-      # read its contents line-by-line (each line is a path) and copy that file to the current assets/ subdir
+      # read its contents line-by-line (each line is a path) and copy that file at that path to the current assets/ subdir
       # note that we only look for assets.external inside the subdirectories, and not in assets/ itself
       assetsubdirectories="$(find /media/bay/taha/chepec/thesis/assets/ -maxdepth 1 -mindepth 1 -type d)"
       # loop through $assetdirs, and look for the file external.assets in each path
@@ -116,10 +117,10 @@ if [ $# -eq 1 ]; then
       echo "<thesis> -------------------------------"
       echo "<thesis> Create low-res photos tree"
       echo "<thesis> -------------------------------"
-      # copy existing photos to assets/photos/.lowres/ path 
+      # copy existing photos to assets/photos/.lowres/ path
       # to save time, rsync only if highres photo has more recent timestamp (otherwise, keep lowres photo without overwriting)
       # Note: rsync usually looks at file timestamp and size, and if either has changed, copies the file (simplified explanation)
-      # in this case, I'd like rsync to only compare timestamps and disregard size 
+      # in this case, I'd like rsync to only compare timestamps and disregard size
       # rsync can't do that. We need to use a different tool. See e.g.
       # https://superuser.com/questions/260092/rsync-switch-to-only-compare-timestamps
       # copy only the "large" photos that have file modtimes more recent than the last time this operation was run