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Runtime-reconfigurable software coupled with reconfigurable hardware is highly desirable as a means towards maximizing runtime efficiency without compromising programmability. Compilers for such software systems are extremely difficult to design as they must leverage different types of hardware at runtime. To address the need for static and dynamic compiler optimization of workflows matched to dynamically reconfigurable hardware, we propose a novel design of the central component of a dynamic software compiler for software defined hardware. Our comprehensive design focuses not just on static knowledge but also on semi-supervised extraction of knowledge from program executions and developing their performance models. Specifically, our novel {\it dynamic and extensible knowledge base} 1) continuously gathers knowledge during execution of workflows 2) identifies {\it optimal} implementations of workflows on {\it optimal} (available) hardware configurations. It plays a hub role in storing information from, and providing information to other components of the compiler, as well as the human analyst. Through a rich tripartite graph representation, the knowledge base captures and learns extensive information on decomposition and mapping of code steps to kernels and mapping of kernels to available hardware configurations. The knowledge base is implemented using the C++ Boost Library and is capable of quickly processing offline and online queries and updates. We show that our knowledge base can answer queries in $1ms$ regardless of the number of workflows it stores. To the best of our knowledge, this is the first design of a dynamic and extensible knowledge base to support compilation of high-level languages to leverage arbitrary reconfigurable platforms.