From 9e458b702f71b2db6adb919d88f93fc0bedc5178 Mon Sep 17 00:00:00 2001
From: Ben Soares <b.soares@dundee.ac.uk>
Date: Wed, 23 Sep 2020 16:48:01 +0100
Subject: [PATCH] JAL-3753 Resources seen in tests and appropriate filters now
 being used as file opt-in rather than opt-out.

---
 build.gradle |   47 ++++++++++++++++++++++++++++-------------------
 1 file changed, 28 insertions(+), 19 deletions(-)

diff --git a/build.gradle b/build.gradle
index 72baea1..072a7b4 100644
--- a/build.gradle
+++ b/build.gradle
@@ -1093,9 +1093,10 @@ task copyDocs(type: Copy) {
   def inputDir = "${jalviewDir}/${doc_dir}"
   def outputDir = "${docBuildDir}/${doc_dir}"
   from(inputDir) {
-    exclude '**/*.gif'
-    exclude '**/*.jpg'
-    exclude '**/*.png'
+    include('**/*.txt')
+    include('**/*.md')
+    include('**/*.html')
+    include('**/*.xml')
     filter(ReplaceTokens,
       beginToken: '$$',
       endToken: '$$',
@@ -1106,14 +1107,14 @@ task copyDocs(type: Copy) {
     )
   }
   from(inputDir) {
-    include '**/*.gif'
-    include '**/*.jpg'
-    include '**/*.png'
+    exclude('**/*.txt')
+    exclude('**/*.md')
+    exclude('**/*.html')
+    exclude('**/*.xml')
   }
   into outputDir
 
   inputs.dir(inputDir)
-  outputs.files(helpFile)
   outputs.dir(outputDir)
 }
 
@@ -1143,9 +1144,12 @@ task copyHelp(type: Copy) {
   def inputDir = helpSourceDir
   def outputDir = "${helpBuildDir}/${help_dir}"
   from(inputDir) {
-    exclude '**/*.gif'
-    exclude '**/*.jpg'
-    exclude '**/*.png'
+    include('**/*.txt')
+    include('**/*.md')
+    include('**/*.html')
+    include('**/*.hs')
+    include('**/*.xml')
+    include('**/*.jhm')
     filter(ReplaceTokens,
       beginToken: '$$',
       endToken: '$$',
@@ -1156,9 +1160,12 @@ task copyHelp(type: Copy) {
     )
   }
   from(inputDir) {
-    include '**/*.gif'
-    include '**/*.jpg'
-    include '**/*.png'
+    exclude('**/*.txt')
+    exclude('**/*.md')
+    exclude('**/*.html')
+    exclude('**/*.hs')
+    exclude('**/*.xml')
+    exclude('**/*.jhm')
   }
   into outputDir
 
@@ -1172,9 +1179,10 @@ task copyResources(type: Copy) {
   def inputDir = resourceDir
   def outputDir = resourcesBuildDir
   from(inputDir) {
-    exclude '**/*.gif'
-    exclude '**/*.jpg'
-    exclude '**/*.png'
+    include('**/*.txt')
+    include('**/*.md')
+    include('**/*.html')
+    include('**/*.xml')
     filter(ReplaceTokens,
       beginToken: '$$',
       endToken: '$$',
@@ -1185,9 +1193,10 @@ task copyResources(type: Copy) {
     )
   }
   from(inputDir) {
-    include '**/*.gif'
-    include '**/*.jpg'
-    include '**/*.png'
+    exclude('**/*.txt')
+    exclude('**/*.md')
+    exclude('**/*.html')
+    exclude('**/*.xml')
   }
   into outputDir
 
-- 
1.7.10.2