linker: Improve handling of unread/unwritten shader inputs/outputs

Previously some shader input or outputs that hadn't received location
assignments could slip through.  This could happen when a shader
contained user-defined varyings and was used with either
fixed-function or assembly shaders.

See the piglit tests glsl-[fv]s-user-varying-ff and
sso-user-varying-0[12].

NOTE: this is a candidate for the 7.9 branch.

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