report open errors properly

[jlaurens]

Some operations require that open or popen succeeds. An assert wrapper is added when necessary.
Without that assert, the error manager reports an attempt to operate on a nil unexpected value.
With that assert, the error manager reports a file system problem.

Summer cleaning:

• local copies of io... functions
• extra local declaration removed
• set file* variables to nil when the file is closed and the variable is used afterwards, ⇒ LLS annotations
• stick to Lua 5.3 ⇒ no more "*a", "*all"
• avoid leaving files open
• consistency: prefer ...:close() instead of close(...)