Boards Manager now install tools even if they are available in the IDE bundle

Previously if a 3rd party core would require a tool already bundled
in the IDE then boards manager skipped the installation of that tool.
This is could lead to missing tools if the IDE is upgraded and the
bundled tools may change.

This patch fixes the bug by always installing tools when needed, even
if they are already bundled.

Author: cmaglie

arduino-core/src/cc/arduino/contributions/packages/ContributionInstaller.java

@@ -79,16 +79,15 @@ public synchronized List<String> install(ContributedPlatform contributedPlatform
     }
 
     // Do not download already installed tools
-    List<ContributedTool> tools = new LinkedList<>(contributedPlatform.getResolvedTools());
-    Iterator<ContributedTool> toolsIterator = tools.iterator();
-    while (toolsIterator.hasNext()) {
-      ContributedTool tool = toolsIterator.next();
+    List<ContributedTool> tools = new ArrayList<>();
+    for (ContributedTool tool : contributedPlatform.getResolvedTools()) {
       DownloadableContribution downloadable = tool.getDownloadableContribution(platform);
       if (downloadable == null) {
         throw new Exception(format(tr("Tool {0} is not available for your operating system."), tool.getName()));
       }
-      if (downloadable.isInstalled()) {
-        toolsIterator.remove();
+      // Download the tool if it's not installed or it's a built-in tool
+      if (!downloadable.isInstalled() || downloadable.isReadOnly()) {
+        tools.add(tool);
       }
     }
 
@@ -125,10 +124,10 @@ public synchronized List<String> install(ContributedPlatform contributedPlatform
 
     List<Map.Entry<ContributedToolReference, ContributedTool>> resolvedToolReferences = contributedPlatform.getResolvedToolReferences().entrySet()
       .stream()
-      .filter((entry) -> !entry.getValue().getDownloadableContribution(platform).isInstalled())
+      .filter((entry) -> !entry.getValue().getDownloadableContribution(platform).isInstalled()
+          || entry.getValue().getDownloadableContribution(platform).isReadOnly())
       .collect(Collectors.toList());
 
-
     int i = 1;
     for (Map.Entry<ContributedToolReference, ContributedTool> entry : resolvedToolReferences) {
       progress.setStatus(format(tr("Installing tools ({0}/{1})..."), i, resolvedToolReferences.size()));

arduino-core/src/cc/arduino/contributions/packages/ContributionsIndexer.java

@@ -374,7 +374,7 @@ public boolean isContributedToolUsed(ContributedPlatform platformToIgnore, Contr
         if (platformToIgnore.equals(platform)) {
           continue;
         }
-        if (!platform.isInstalled()) {
+        if (!platform.isInstalled() || platform.isReadOnly()) {
           continue;
         }
         for (ContributedTool requiredTool : platform.getResolvedTools()) {