make ott after make clean fails

[kcranston]

make clean:

(base) kcranston@otree3:~/reference-taxonomy$ make clean
rm -f `find . -name "*.class"`
rm -rf bin/jython
rm -rf r/*/resource r/*/source r/*/work
rm -rf config.mk
rm -rf r/*-NEW
rm r/*-HEAD r/*-PREVIOUS
rm -rf tmp *.tmp properties
rm -rf t/amendments t/tax/aster

make ott:

(base) kcranston@otree3:~/reference-taxonomy$ make ott
mkdir -p bin
(echo "#!/bin/bash"; \
 echo "export JYTHONPATH=.:$PWD:$PWD/util:$PWD/lib/json-simple-1.1.1.jar"; \
 echo '[ "x$JAVAFLAGS" = x ] && JAVAFLAGS="-Xmx14G"'; \
 echo exec java '$JAVAFLAGS' -jar $PWD/lib/jython-standalone-2.7.0.jar '$*') >bin/jython
chmod +x bin/jython
javac -g -classpath ".:lib/*" org/opentreeoflife/taxa/Taxonomy.java org/opentreeoflife/taxa/CSVReader.java org/opentreeoflife/taxa/Node.java org/opentreeoflife/taxa/Newick.java org/opentreeoflife/taxa/InterimFormat.java org/opentreeoflife/taxa/SimpleMap.java org/opentreeoflife/taxa/Rank.java org/opentreeoflife/taxa/EventLogger.java org/opentreeoflife/taxa/Answer.java org/opentreeoflife/taxa/Nexson.java org/opentreeoflife/taxa/QualifiedId.java org/opentreeoflife/taxa/Taxon.java org/opentreeoflife/taxa/HomonymReport.java org/opentreeoflife/taxa/Addition.java org/opentreeoflife/taxa/CSVWriter.java org/opentreeoflife/taxa/Synonym.java org/opentreeoflife/taxa/SourceTaxonomy.java org/opentreeoflife/taxa/TsvEdits.java org/opentreeoflife/taxa/Flag.java org/opentreeoflife/smasher/Alignment.java org/opentreeoflife/smasher/AlignmentByName.java org/opentreeoflife/smasher/AlignmentByMembership.java org/opentreeoflife/smasher/MergeMachine.java org/opentreeoflife/smasher/Reportx.java org/opentreeoflife/smasher/UnionTaxonomy.java org/opentreeoflife/smasher/Test.java org/opentreeoflife/smasher/Heuristic.java org/opentreeoflife/smasher/Smasher.java org/opentreeoflife/conflict/ConflictAnalysis.java org/opentreeoflife/conflict/Articulation.java org/opentreeoflife/conflict/Disposition.java org/opentreeoflife/server/Services.java
make: *** No rule to make target 'r/idlist-HEAD/source/.made', needed by 'r/ott-NEW/source/debug/transcript.out'.  Stop.

This is likely related to #365

[kcranston]

If, after a make clean, you instead start over building ott3.1 following the instructions you get the following error after the make refresh/idlist: Collision: idlist-3.0 already exists. Please pick a different version label

So make clean is not quite cleaning up everything.