codeql run test doesn't match absolute fs paths in graph queries

Per @max-schaefer `codeql run test` should adapt queries that emit absolute FS paths such that they pass when run in a different environment. For example my test emits `# 0| [File] /home/chris/codeql-home/codeql-go/ql/test/library-tests/semmle/go/PrintAst/input.go` but the test doesn't work when the `.expected` file uses a truncated relative version of that path, or when it uses a different absolute path and the .actual uses the absolute path appropriate to a different environment.

Begin at the `codeql run test` entry point and reproduce the absolute-path mismatch described in the issue. Determine how expected and actual output should be normalized across environments; done means the example passes with relative or differing absolute paths while preserving other output comparisons.

Written by the indexing model from the issue text.