FPGA Development Guide

A typical work-flow for FPGA design may be separated into three main stages:

Architecture
Describing your design at various levels of abstraction. The most basic components, from synchronisers to simple processors, are written in an HDL, such as SystemVerilog; these are then combined (recursively) to form more complex systems.
Simulation and Synthesis
Simulation tests your design by emulating hardware matching the semantics of the HDL. Synthesis is the compilation of your design into a netlist, expressing it in terms of FPGA elements (e.g. wiring, LUTs, etc.).
Software
Processor architectures can run programs compiled to the appropriate binary (machine code) format. A binary is executed by reading its instructions from the device memory; some binaries may be incorporated into the device programming file, others uploaded dynamically.

A general overview is given by the following schematic; the labs provide greater coverage.

FPGA Development Schematic
Eclipse
Software IDE. Includes a C compiler producing binaries (machine code) for the NIOS II processor.
HAL
Hardware Abstraction Layer. A NIOS II Eclipse project providing a low-level, memory-mapped interface to a specified architecture. The interface is basically a set of constants defining address ranges to which each component is mapped, and procedures to read and write data.
Quartus
Hardware IDE. Using an HDL, such as SystemVerilog, a Quartus project is a hierarchy of components or modules from a specified root. A complete project may be synthesised for programming onto a specified FPGA device.
Qsys
Qsys works at the component level of abstraction. A component in Qsys is a black box with a specified interface (wires), which can be connected together using a switched interconnect memory system. Each black box is ultimately a set of files in some HDL. Each Qsys project thus represents a hierarchy of Verilog components (much like a Quartus project), meaning it can also be treated as a component for use in another project.
Modelsim
Provides a simulation environment for (System)Verilog containing debug code (ignored for synthesis).
Programmer / tPad
JTAG is a communications protocol for on-chip debug (e.g. via a JTAG UART) and programming, using a standard group of dedicated pins. The FPGA is primarily configurable as a switch fabric and lookup tables, the former controlling connections between wires and the latter implementing custom functions. The control logic of each configurable element is memory-mapped to a dedicated SRAM module. An SRAM Object File (.sof), produced by a Quartus compilation, contains configuration data for each element, which is loaded via JTAG into the corresponding (volatile) SRAM module to (temporarily) program the FPGA.