Complete PdeProjectJar bin.includes and output prefix handling

[laeubi]

Make PdeProjectJar bin.includes-driven instead of blindly iterating output.* entries. Handle dot entry with fallback to JDT default output folder for Java projects, package non-dot libraries as embedded inner jars via JarResource, and include regular files/folders from project.

[eclipse-pde-bot]

This pull request changes some projects for the first time in this development cycle.
Therefore the following files need a version increment:

ui/org.eclipse.pde.launching/META-INF/MANIFEST.MF

An additional commit containing all the necessary changes was pushed to the top of this PR's branch. To obtain these changes (for example if you want to push more changes) either fetch from your fork or apply the git patch.

Git patch

From 209798509771e9f1cdfce9c6afa84232ebf627bf Mon Sep 17 00:00:00 2001
From: Eclipse PDE Bot <pde-bot@eclipse.org>
Date: Sun, 8 Mar 2026 09:20:53 +0000
Subject: [PATCH] Version bump(s) for 4.40 stream


diff --git a/ui/org.eclipse.pde.launching/META-INF/MANIFEST.MF b/ui/org.eclipse.pde.launching/META-INF/MANIFEST.MF
index 45e9365482..4d331f7d01 100644
--- a/ui/org.eclipse.pde.launching/META-INF/MANIFEST.MF
+++ b/ui/org.eclipse.pde.launching/META-INF/MANIFEST.MF
@@ -2,7 +2,7 @@ Manifest-Version: 1.0
 Bundle-ManifestVersion: 2
 Bundle-Name: %name
 Bundle-SymbolicName: org.eclipse.pde.launching;singleton:=true
-Bundle-Version: 3.13.600.qualifier
+Bundle-Version: 3.13.700.qualifier
 Bundle-RequiredExecutionEnvironment: JavaSE-17
 Bundle-Vendor: %provider-name
 Require-Bundle: org.eclipse.jdt.junit.core;bundle-version="[3.6.0,4.0.0)",
-- 
2.53.0

Further information are available in Common Build Issues - Missing version increments.

[github-actions]

Test Results

  147 files  ±0    147 suites  ±0   36m 0s ⏱️ +54s
3 482 tests ±0  3 428 ✅ ±0   54 💤 ±0  0 ❌ ±0 
9 270 runs  ±0  9 140 ✅ ±0  130 💤 ±0  0 ❌ ±0 

Results for commit d0df398. ± Comparison against base commit b0680cf.

[laeubi]

Only Timeout warning for P2 download