Software and hardware co-design and optimization of HPC systems has become intolerably complex, ad-hoc, time consuming and error prone due to enormous number of available design and optimization choices, complex interactions between all software and hardware components, and multiple strict requirements placed on performance, power consumption, size, reliability and cost. We present our novel long-term holistic and practical solution to this problem based on customizable, plugin-based, schema-free, heterogeneous, open-source Collective Mind repository and infrastructure with unified web interfaces and on-line advise system. This collaborative framework distributes analysis and multi-objective off-line and on-line auto-tuning of computer systems among many participants while utilizing any available smart phone, tablet, laptop, cluster or data center, and continuously observing, classifying and modeling their realistic behavior. Any unexpected behavior is analyzed using shared data mining and predictive modeling plugins or exposed to the community at cTuning.org for collaborative explanation, top-down complexity reduction, incremental problem decomposition and detection of correlating program, architecture or run-time properties (features). Gradually increasing optimization knowledge helps to continuously improve optimization heuristics of any compiler, predict optimizations for new programs or suggest efficient run-time (online) tuning and adaptation strategies depending on end-user requirements. We decided to share all our past research artifacts including hundreds of codelets, numerical applications, data sets, models, universal experimental analysis and auto-tuning pipelines, self-tuning machine learning based meta compiler, and unified statistical analysis and machine learning plugins in a public repository to initiate systematic, reproducible and collaborative R\&D with a new publication model where experiments and techniques are validated, ranked and improved by the community.