Known limitations

agentic-proteins preserves a historically broad caller surface. Its compatibility value is real, but it is not evidence that the bridge is already thin, that every path is a direct alias, or that new integrations should use it.

Current limits

Limitation	Consequence	Responsible interpretation
the source tree contains legacy agents, providers, tools, state, execution, orchestration, CLI, and HTTP paths	compatibility spans more than a single import facade	inspect the exact path; do not infer whole-package equivalence from one forwarding test
top-level Runtime exports are identity-tested, but nested historical paths have different proof	one verified alias does not establish every nested module as a pure alias	require path-specific comparison evidence
execution and orchestration both remain visible	similar names can obscure which surface is canonical	treat Runtime as owner and consult bridge contracts before extending either path
optional local and remote providers depend on external systems and extras	availability, latency, failure, and reproducibility vary by environment	record provider, version, configuration, and failure outcome
CLI and HTTP compatibility preserve transport obligations	transport success does not prove scientific validity of a result	inspect run state, artifacts, warnings, and downstream scientific evidence
retirement depends on downstream callers	repository-local green tests cannot prove that no external consumer remains	keep caller and removal evidence explicit

Proof boundary

flowchart TD
    T["verified top-level forwarding"] --> I["import compatibility"]
    T -. does not imply .-> N["all nested paths are aliases"]
    I -. does not imply .-> S["scientific result validity"]
    B["behavioral comparison"] --> P["bounded path parity"]
    P -. does not imply .-> R["safe retirement without caller evidence"]

A successful bridge call says that the tested compatibility route completed under the recorded conditions. It does not say that an optional provider was available everywhere, that every artifact has equivalent scientific meaning, or that the corresponding legacy surface can be removed.

How to report a gap

Name the precise path and missing proof: for example, “top-level RunManager identity is verified; nested HTTP error parity was not evaluated.” Avoid package-wide phrases such as “fully equivalent” unless every public surface, negative path, and retained artifact in that claim has direct evidence.

The durable destination is Bijux Proteomics Runtime. The bridge remains supported only within the explicit compatibility contract.