Standardise .gitignore across BEAST3 packages

Add BEAST run output patterns (*.log, *.trees, *.xml.state),
package ZIP pattern, and ensure .idea/*.iml are ignored.

Author: alexeid

.gitignore

@@ -1,32 +1,24 @@
-### Maven ###
+.DS_Store
+
+# Build output
+/out
+/bin
 target/
+**/target/
 
-### IntelliJ IDEA ###
-out/
-!**/src/main/**/out/
-!**/src/test/**/out/
+# IntelliJ
+/.idea
+*.iml
 
-### Eclipse ###
-.apt_generated
+# Eclipse
 .classpath
-.factorypath
 .project
-.settings
-.springBeans
-.sts4-cache
-bin/
-!**/src/main/**/bin/
-!**/src/test/**/bin/
-
-### NetBeans ###
-/nbproject/private/
-/nbbuild/
-/dist/
-/nbdist/
-/.nb-gradle/
+/build
 
-### VS Code ###
-.vscode/
+# BEAST run output
+*.log
+*.trees
+*.xml.state
 
-### Mac OS ###
-.DS_Store
+# Package ZIPs
+*.v*.zip