Optical networks are designed to be operated statically: lightpaths are provisioned for uninterrupted operation for several years using high margins to anticipate the deterioration of their quality of transmission (QoT) from various factors (equipment aging, malfunctioning, and maintenance operations). Operating the network dynamically and closer to its actual capabilities increases efficiency and reduces capital expenditure. We develop a cross-layer QoT-aware toolkit that leverages monitoring information and the flexibility dimensions of elastic optical networks. It adapts the network's parameters and regulates the QoT to achieve high efficiency. The toolkit can be used in a plethora of use cases in the deployment or during the operation phase of the network, e.g., to harvest the excessive margins when lightpaths are initially deployed or failures are repaired, to adapt the network to changing traffic demands, and to restore margins when soft failures such as equipment malfunction or aging render the QoT of certain lightpaths unacceptable. In the last case, the toolkit can be used to appropriately reconfigure the lightpaths to restore their QoT and postpone the deployment of regenerators, as indicated by our simulations.