Refactor/restructure directories (#150)

* refactor: rename folder embedded -> src

* chore(git): merge src/.gitignore with root .gitignore

* refactor(vscode): move src/.vscode to .vscode

* chore(vscode): update include paths

* refactor: move .svd files to new /debug folder

* chore(vscode): hide .mxproject files from file explorer

* refactor: move Makefile to repo root

* build: update Makefile paths for new directory structure

* refactor: move src/Scripts to /scripts folder

* chore(vscode): update script paths

* chore(trunk): update source paths

* build: update paths in compile commands generation script