The "Transform Tool" lets you select an object and manipulate its handle (move, rotate or scale).
Clicking an object in the canvas window with the "Transform tool" selects it. You can select multiple objects by holding down the Control key and clicking on the additional objects.
If the layer is a "no edge layer" (gradient for example) you cannot click on the layers below, even if you have clicked in the transparent area of the layer. This allow to select only current visible layers. Consider also that some layers have not yet defined a way to click on them to be selected (Text Layer for example).
If, with the "Transform Tool", you can not select an object because it is obscured by another object you can select its layer in the Layers Panel.
Once a layer is selected, its Handle is displayed.
The "Transform tool" works on selected handles only.
Click on a handle to select it. A selected handle becomes highlighted. You can select more handles by Ctrl Click on each one. You can also drag a Selection box around the handles to select them.
ControlA will select all handles in the selected layers. (ControlD will deselect all handles)
Dragging a Selection box while pressing Ctrl will toggle handle selection. Currently selected handles within the Selection box will become deselected and currenly non selected handles will become selected.
Clicking on selected handles with the "Transform tool" will allow you to drag them around in the canvas. Make sure you click on them, clicking outside will deselect the handles.
Pressing ⇧ Shift while dragging allows you to restrict the movement to the X or Y coordinates.
Pressing Ctrl while clicking handles will allow you to rotate them around a calculated center for the currently selected handles.
Pressing Alt while dragging handles will scale them around their calculated common centre. Pressing ⇧ Shift while scaling will preserve the ratio of the handles.
If you want to constrain a tangent handle to X or Y movement you have to press ⇧ Shift after you start to drag it.
Otherwise, pressing ⇧ Shift before dragging a tangent will split it into separate left and right tangents.
Historical note about Synfig
The "Transform Tool" was called the "Normal Tool" before Synfig version 0.62.01.