Scope and Non-Goals

agentic-proteins preserves named historical access to behavior now owned by bijux-proteomics-runtime. Its scope is defined by observable caller contracts: imports, the console command, HTTP application construction, optional extras, exceptions, and retained runtime artifacts. It is not a second runtime implementation.

In Scope

Supported concern	Compatibility obligation	Canonical authority
root exports	historical and canonical imports resolve to the promised object identity	Runtime public API
nested imports listed in the migration ledger	path remains importable or fails through an explicit compatibility decision	owning Runtime module
agentic-proteins executable	command tree, options, defaults, exit behavior, output envelopes, and artifacts match Runtime	Runtime CLI
HTTP application factory	routes, middleware, dependencies, errors, and lifecycle behavior remain equivalent	Runtime HTTP surface
optional extras	a historical extra selects the matching Runtime capability or reports its absence clearly	Runtime provider boundary
warnings and migration guidance	callers receive a canonical replacement without altered successful behavior	compatibility package

Out Of Scope

• new providers, orchestration rules, retry policy, state machines, persistence, output formats, or HTTP behavior;
• scientific models or acceptance policy owned by Core;
• evidence, recommendation, or laboratory policy;
• a legacy-only interpretation of Runtime state or artifacts; and
• removal based only on repository search, elapsed time, or package-local green tests.

flowchart LR
    caller["historical caller"] --> bridge["compatibility surface"]
    bridge --> runtime["canonical Runtime owner"]
    runtime --> result["result, state, and artifacts"]
    bridge -. "must not create" .-> alternate["alternate runtime policy"]

Decide where a change belongs

Proposed change	Decision
add or change runtime behavior	implement and prove it in Runtime first
restore a documented historical path	add the narrowest forwarding route and parity evidence here
translate an old argument or result	require an explicit adapter contract; never present translation as object identity
preserve old durable state	decode through a Runtime-owned schema; do not make the bridge a state owner
remove a path	require canonical replacement, caller evidence, release communication, and negative import proof

The boundary is satisfied only when a reviewer can name the historical surface, canonical destination, parity dimensions, remaining callers, and removal condition. Unknown callers keep a supported surface open; they do not justify adding new bridge-owned behavior.