[brendan-m-murphy]

Fixes #223.

Ensures cached class definitions still emit SymbolInformation and records identity-only information for undocumented external symbols. Retains the reported reproduction and structural regression checks.

Empty external records can acquire documentation from later visits; populated records are never replaced by empty placeholders. This avoids making documentation depend on import order. Local modules shadowing installed packages must not acquire external records.

External-symbol metadata is optional in SCIP. The structural checks establish this project's compatibility expectations; they are not a claim that every external reference requires metadata under the protocol.

Verification

• Added real-indexing checks for both import numbers / from numbers import Real orders and a local module shadowing an installed package.
• Production/development builds, all 22 snapshot tests, all 7 SCIP Jest tests, and formatting passed locally on Linux with Node 24.4.1 and Python 3.10.22.
• The existing Linux/macOS snapshot workflow now also runs the SCIP Jest suite after installation/build; previously it omitted that suite.
• The OpenGHG/SQLite measurements in the contributor's comment are separate contributor-reported evidence, not independently repeated in this validation. Native Windows/macOS execution was not performed locally.

[brendan-m-murphy]

I know it's bad form... but this is one-shot from codex. This PR does fix the bug I encountered though:

I tested this fix against OpenGHG, a medium-sized Python package for processing atmospheric greenhouse-gas measurement and modelling data.

Using the same OpenGHG checkout and scip-cli 2.7.0:

• Released scip-python 0.6.6 indexed 275 files, but conversion to SQLite failed because VersioneerBadRootError# had a definition occurrence without corresponding SymbolInformation.
• A build from this PR also indexed 275 files and converted successfully.
• The resulting 7.2 MB database contained 6,666 global symbols and 18,650 mentions.
• As a functional check, scip-cli successfully resolved Datasource.add_timed_data to its definition in openghg.objectstore._legacy_datasource.

This is a controlled before/after test and confirms that the PR fixes the missing-SymbolInformation failure on a real-world Python codebase.

(Again, apologies for the AI generated summary... scip-python seems useful and I want to try it out, but I don't have time to dig into the code myself.)