Replace extra_files_path with files_path.

Bjoen: As far as I know, that is now the recommended way. And
extra_files_path seems to be broken in conjunction with the
object store.

Peter: Confirmed with @jmchilton on pull request #44 discussion
that this is now the preferred way to do this.

tools/ncbi_blast_plus/ncbi_dustmasker_wrapper.xml

@@ -13,7 +13,7 @@ dustmasker
 #if $db_opts.db_opts_selector == "db":
   -in "${db_opts.database.fields.path}" -infmt blastdb
 #elif $db_opts.db_opts_selector == "histdb":
-  -in "${os.path.join($db_opts.histdb.extra_files_path, 'blastdb')}" -infmt blastdb
+  -in "${os.path.join($db_opts.histdb.files_path, 'blastdb')}" -infmt blastdb
 #else:
   -in "$subject" -infmt fasta
 #end if

tools/ncbi_blast_plus/ncbi_macros.xml

@@ -351,7 +351,7 @@
 #if $db_opts.db_opts_selector == "db":
   -db "${db_opts.database.fields.path}"
 #elif $db_opts.db_opts_selector == "histdb":
-  -db "${os.path.join($db_opts.histdb.extra_files_path,'blastdb')}"
+  -db "${os.path.join($db_opts.histdb.files_path,'blastdb')}"
 #else:
   -subject "$db_opts.subject"
 #end if

tools/ncbi_blast_plus/ncbi_makeblastdb.xml

@@ -10,7 +10,7 @@
 ##and abort (via the ampersand ampersand trick) if any are found.
 #for i in $input_file#"${i}" #end for#
 &&
-makeblastdb -out "${os.path.join($outfile.extra_files_path,'blastdb')}"
+makeblastdb -out "${os.path.join($outfile.files_path,'blastdb')}"
 $parse_seqids
 $hash_index
 ## Single call to -in with multiple filenames space separated with outer quotes

tools/ncbi_blast_plus/ncbi_rpsblast_wrapper.xml

@@ -15,7 +15,7 @@ rpsblast
 #if $db_opts.db_opts_selector == "db":
   -db "${db_opts.database.fields.path}"
 #elif $db_opts.db_opts_selector == "histdb":
-  -db "${os.path.join($db_opts.histdb.extra_files_path,'blastdb')}"
+  -db "${os.path.join($db_opts.histdb.files_path,'blastdb')}"
 #end if
 -evalue $evalue_cutoff
 @BLAST_OUTPUT@

tools/ncbi_blast_plus/ncbi_rpstblastn_wrapper.xml

@@ -15,7 +15,7 @@ rpstblastn
 #if $db_opts.db_opts_selector == "db":
   -db "${db_opts.database.fields.path}"
 #elif $db_opts.db_opts_selector == "histdb":
-  -db "${os.path.join($db_opts.histdb.extra_files_path,'blastdb')}"
+  -db "${os.path.join($db_opts.histdb.files_path,'blastdb')}"
 #end if
 -evalue $evalue_cutoff
 @BLAST_OUTPUT@