Xilinx documents one should be familiar with:

### UG470: 7 Series FPGAs Configuration User Guide

Chapter 5: Configuration Details contains a good description of the overall bit-stream format. (See section “Bitstream Composition” and following.)

### UG912: Vivado Design Suite Properties Reference Guide

Contains an excellent description of the in-memory data structures and associated properties Vivado uses to describe the design and the chip. The TCL interface provides a convenient interface to access this information.

### UG903: Vivado Design Suite User Guide: Using Constraints

The fuzzers generate designs (HDL + Constraints) that use many physical contraints constraints (placement and routing) to produce bit-streams with exactly the desired features. It helps to learn about the available constraints before starting to write fuzzers.

### UG901: Vivado Design Suite User Guide: Synthesis

Chapter 2: Synthesis Attributes contains an overview of the Verilog attributes that can be used to control Vivado Synthesis. Many of them are useful for writing fuzzer designs. There is some natural overlap with UG903.

### UG909: Vivado Design Suite User Guide: Partial Reconfiguration

Among other things this UG contains some valuable information on how to constrain a design in a way so that the items inside a pblock are strictly separate from the items outside that pblock.

### UG474: 7 Series FPGAs Configurable Logic Block

Describes the capabilities of a CLB, the most important non-interconnect resource of a Xilinx FPGA.

Other documentation that might be of use:

Doc of .bit container file format:

Open-Source Bitstream Generation for FPGAs, Ritesh K Soni, Master Thesis:

VTR-to-Bitstream, Eddie Hung:

From the bitstream to the netlist, Jean-Baptiste Note and Éric Rannaud:

Wolfgang Spraul’s Spartan-6 (xc6slx9) project:

Marek Vasut’s Typhoon Cyclone IV project:

XDL generator/imported for Vivado: