fix(gui): fix IndexOutOfBoundsException when switching between tabs via mouse wheel (#1456)(PR #1469)

* feat: Add option to include/exclude dependencies when saving
* fix save skip for class depencencies
Co-authored-by: NSkylot <skylot@gmail.com>

* fix(gui): NullPointerException on project save

* chore(gui): ensure MainWindow.project is never null
* ensure `files` in `ProjectData` in not null
Co-authored-by: NSkylot <skylot@gmail.com>

fix(res): ignore resource chunk entries that are located after the resource chunk end (#751)(PR #1436)

* remove <code> tags from appdata.xml because flatpak doesn't like it
* appdata.xml: remove <a> tag because flatpak doesn't like it

* chore: better variable naming for getInstance calls
* chore: rebalance preferences window and fix empty plugins section directly after jadx-gui start
* chore: do not ask for project save if nothing had been changed
* use parallel mode for gradle
* minor improvements for app debugging
* apply CodeQL suggestion to prevent log injection
* handle IntelliJ Idea warnings
* replace not-ASCII chars in LogUtils.escape
Co-authored-by: NSkylot <skylot@gmail.com>

* fix(debugger): several IO read problems fixed
* merged latest changes
* fixed read loop
* Update jadx-gui/src/main/java/jadx/gui/device/protocol/ADB.java
Co-authored-by: Nskylot <118523+skylot@users.noreply.github.com>