I use a simple spreadsheet for anything.
Although I have done many years of DVT testing since the early 80's for high level products such as computer systems, and reverse engineering tests of Disk drives, it basically comes down to verifying the product specifications and measuring the margin of exceeding any specification under worst case.
Honestly I don't have much FPGA experience, but when I once designed a head-mounted display ( circa '99) using the Kopin VGA chip to view any laptop in VGA mode or any VCR or TV analog signal , I chose an Altera FPGA and wrote all the requirements in simple high level structures on paper for H sync, Vsync and routing the RGB analog signals.
A test engineer in my dept, who specialized in ATE had no Altera experience but succeeded in applying the same test principles used in ATE by generating a vector test table to verify the design.
It took me a couple months from concept to delivery of the 1st working prototype while our Customer Service Mgr who was also a Mech. Eng did the mechanical CAD design for the plastic housing in his spare time. He got SLA samples overnight and I got PCB samples in 1 day. It was the smallest TV monitor in the world at that time and we beat Motorola in show N tell at COMDEX for demonstrating how to read a fax on cell phone or an ultrasonic display on the eye TV headset. ( more clunky than Google's glasses but it worked. ) It was called the M1.
So you can invent your own method as long as you have well defined specifications and can translate them into code and verify it against all variables such as timing race conditions, thermal effects, shock and vibration effects and power supply noise.
For code, I like the GitHub cloud method of change control when collaboration is required. But for individual needs anything will do. But to work in a large organization collaboration is essential.
The best tool is the one you know how to use well and is scale-able to large projects and organizations.
BTW San Jose used to have jobs like this about an inch thick in the Sunday Mercury News when I used to travel to Silicon Valley all the time.....
You don't need 5 yrs experience. You just need to learn how to do anything well and then quickly. DIY learning is my motus operandi, consequently I invented many things before their time, including SCADA in '77 using a pair of HP9825s and mapping the keyboard into a rocket launchpad payload controller.
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To define all the HR requirements look at some popular tools like
http://www.bamboohr.com/?utm_source=RevSite-CapterraHRS-Demo#scheduledemo
Then rank your priority list for yourself and your "customers" to separate the MUST haves from the NICETOHAVES to hammer out a spec.