Low-Power Wide-Area Networks (LPWANs) are an emerging Internet-of-Things (IoT) paradigm, which caters to large-scale and long-term sensory data collection demand. Among the commercialized LPWAN technologies, LoRa (Long Range) attracts much interest from academia and industry due to its open-source physical (PHY) layer and standardized networking stack. In the flourishing LoRa community, many observations and countermeasures have been proposed to understand and improve the performance of LoRa networking in practice. From the perspective of the LoRa networking stack; however, we lack a whole picture to comprehensively understand what has been done or not and reveal what the future trends are. This survey proposes a taxonomy of a two-dimensional (i.e., networking layers, performance metrics) to categorize and compare the cutting-edge LoRa networking techniques. One dimension is the layered structure of the LoRa networking stack. From down to the top, we have the PHY layer, Link layer, Media-access Control (MAC) layer, and Application (App) layer. In each layer, we focus on the three most representative layer-specific research issues for fine-grained categorizing. The other dimension is LoRa networking performance metrics, including range, throughput, energy, and security. We compare different techniques in terms of these metrics and further overview the open issues and challenges, followed by our observed future trends. According to our proposed taxonomy, we aim at clarifying several ways to achieve a more effective LoRa networking stack and find more LoRa applicable scenarios, leading to a brand-new step toward a large-scale and long-term IoT.