update makefile

Makefile

@@ -1,24 +1,24 @@
-ROOT_DIR:=$(shell dirname $(realpath $(firstword $(MAKEFILE_LIST))))
+ROOT_DIR:=$(shell pwd)
 ANTLR_VERSION=9
 
 all : download_antlr_jar draft2 v1 v1_1 v2
 
 download_antlr_jar:
-	(if [ ! -e ${ROOT_DIR}/antlr-4.${ANTLR_VERSION}-complete.jar ]; then \
+	(if [ ! -e "${ROOT_DIR}/antlr-4.${ANTLR_VERSION}-complete.jar" ]; then \
 		wget https://www.antlr.org/download/antlr-4.${ANTLR_VERSION}-complete.jar; \
 	fi)
 
 draft2 :
-	(cd ${ROOT_DIR}/src/main/antlr4/draft_2;  java -jar ${ROOT_DIR}/antlr-4.${ANTLR_VERSION}-complete.jar -o ${ROOT_DIR}/src/main/java -visitor -package org.openwdl.wdl.parser.draft_2 WdlDraft2Parser.g4 WdlDraft2Lexer.g4)
+	(cd "${ROOT_DIR}/src/main/antlr4/draft_2";  java -jar "${ROOT_DIR}/antlr-4.${ANTLR_VERSION}-complete.jar" -o "${ROOT_DIR}/src/main/java" -visitor -package org.openwdl.wdl.parser.draft_2 WdlDraft2Parser.g4 WdlDraft2Lexer.g4)
 
 v1 :
-	(cd ${ROOT_DIR}/src/main/antlr4/v1; java -jar ${ROOT_DIR}/antlr-4.${ANTLR_VERSION}-complete.jar -o ${ROOT_DIR}/src/main/java -visitor -package org.openwdl.wdl.parser.v1 WdlV1Parser.g4 WdlV1Lexer.g4)
+	(cd "${ROOT_DIR}/src/main/antlr4/v1"; java -jar "${ROOT_DIR}/antlr-4.${ANTLR_VERSION}-complete.jar" -o "${ROOT_DIR}/src/main/java" -visitor -package org.openwdl.wdl.parser.v1 WdlV1Parser.g4 WdlV1Lexer.g4)
 
 v1_1 :
-	(cd ${ROOT_DIR}/src/main/antlr4/v1_1; java -jar ${ROOT_DIR}/antlr-4.${ANTLR_VERSION}-complete.jar -o ${ROOT_DIR}/src/main/java -visitor -package org.openwdl.wdl.parser.v1_1 WdlV1_1Parser.g4 WdlV1_1Lexer.g4)
+	(cd "${ROOT_DIR}/src/main/antlr4/v1_1"; java -jar "${ROOT_DIR}/antlr-4.${ANTLR_VERSION}-complete.jar" -o "${ROOT_DIR}/src/main/java" -visitor -package org.openwdl.wdl.parser.v1_1 WdlV1_1Parser.g4 WdlV1_1Lexer.g4)
 
 v2 :
-	(cd ${ROOT_DIR}/src/main/antlr4/v2; java -jar ${ROOT_DIR}/antlr-4.${ANTLR_VERSION}-complete.jar -o ${ROOT_DIR}/src/main/java -visitor -package org.openwdl.wdl.parser.v2 WdlV2Parser.g4 WdlV2Lexer.g4)
+	(cd "${ROOT_DIR}/src/main/antlr4/v2"; java -jar "${ROOT_DIR}/antlr-4.${ANTLR_VERSION}-complete.jar" -o "${ROOT_DIR}/src/main/java" -visitor -package org.openwdl.wdl.parser.v2 WdlV2Parser.g4 WdlV2Lexer.g4)
 
 clean :
 	rm -rf src/main/java

doc/Commands/Fix.md

@@ -83,9 +83,6 @@ Fix specification incompatibilities in WDL file and all its dependencies.
 Options:
 
   -a, --antlr4-trace          enable trace logging of the ANTLR4 parser
-  -b, --base-uri  <arg>       Base URI for imports; output directories will be
-                              relative to this URI; defaults to the parent
-                              directory of the main WDL file
   -f, --follow-imports        (Default) format imported files in addition to the
                               main file
       --nofollow-imports      only format the main file