stage2: more Decl lifetime fixes

 * File stores `root_decl: Decl` instead of `namespace: *Namespace`.
   This maps more cleanly to the actual ownership, since the `File` does
   own the root decl, but it does not directly own the `Namespace`.
 * `semaFile` completes the creation of the `Decl` even when semantic
   analysis fails. The `analysis` field of the `Decl` will contain the
   results of semantic analysis. This prevents cleaning up of memory
   still referenced by other Decl objects.
 * `semaDecl` sets `Struct.zir_index` of the root struct decl, which
   fixes use of undefined value in case the first update contained a ZIR
   compile error.

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