Algorithm/tool caching and removal of hashes in names

• introduced class stores for tools/algorithms to have earlier deduplication
• same conf, different names -> failure
• fixed some bugs
• more checks, you cannot give plain Configurables as inputs to an Algorithm/Tool constructor
• formatting
• added unique names without hashes

closes #30 (closed)
closes #12 (closed)
closes #31 (closed)
closes #26 (closed)