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Current Capability Limits

This page is the repository honesty boundary. It names where the current scientific, runtime, grounding, recommendation, and lab-consequence chain still stops stronger public language.

The point is not to deny progress. The repository is materially deeper than it was at v0.3.7. The point is to keep the wording tied to the weakest live owner surface instead of letting stronger neighboring surfaces inflate the claim.

Current Family-Level Ceiling

family strongest current honest sentence main limiting layer
dda outsider-auditable, bounded runtime realism remains weaker than in-repo live-engine parity
dia outsider-auditable, bounded benchmark and runtime strength still narrow under library incompleteness and consequence pressure
lfq review-grade, bounded external review, normalization, and transfer pressure still block wider language
multiplex internal support only outsider trust still collapses under the current stress packet
ptm outsider-auditable, bounded localization evidence remains stronger than consequence confidence
targeted outsider-auditable, bounded calibration, interference, and downstream burden still narrow the sentence

Repository-Wide Limits

  • several families are now publicly challengeable, but there is still no repository-wide proof set that supports broad proteomics authority under the same standard
  • stronger core biology and chemistry coverage does not by itself erase transfer, runtime, or consequence limits
  • one strong family packet does not widen the sentence for weaker families
  • recommendation posture still narrows when grounded contradiction or downstream assay burden becomes explicit

Which Layer Currently Carries The Brake

layer what is already strong why it still does not widen the sentence alone
core broader biology, chemistry, spectra, mzML, PTM, DIA, and quantification depth stronger scientific machinery still needs transfer, runtime, and downstream proof
runtime replay, rerun kits, artifact stability, refusal, comparability reproducible runs do not settle scientific truth or assay worth
knowledge grounding, contradiction, citation pressure, biological context grounded sentences can still be analytically overconfident or too costly to act on
intelligence challenge, downgrade, regret, recommendation posture stronger analytical policy cannot outrun weaker benchmark, grounding, or consequence layers
lab control demand, readiness, refusal, outcome reconciliation practical follow-up can still be too narrow to justify broader public release language

Why The Limits Sit In Different Layers

The current ceiling is not caused by one kind of weakness only:

  • some limits are benchmark-transfer limits
  • some are runtime-lane and execution-realism limits
  • some are grounded-claim and contradiction limits
  • some are recommendation-pressure and regret limits
  • some are lab-readiness and consequence-burden limits

That is why no single package can honestly declare the whole repository ready on its own.

Where The Repository Is Clearly Stronger Now

  • core is materially deeper across sequence, chemistry, spectra, mzML, DIA, PTM review, and quantification
  • runtime now has real replay, rerun, refusal, and artifact-stability routes
  • knowledge and intelligence now expose grounded contradiction, downgrade, and recommendation-pressure surfaces directly
  • lab now makes control demand, refusal, and requested-versus-observed follow-up visible enough to limit public language honestly

These improvements matter. They also make the honesty boundary more important, not less.

What Stronger Code Still Does Not Automatically Earn

  • broad cross-family release language
  • decision-grade recommendation authority
  • vendor-parity execution claims
  • universal transfer across study design, instrument class, or sample complexity
  • stronger lab-confidence language than the current follow-up burden supports

What Would Need To Improve Before Language Widens

  • stronger family-specific transfer packets where benchmark depth is currently narrower than the release sentence
  • runtime proof that survives more realism pressure where import_only or bounded raw_executable lanes still cap trust
  • grounding routes that keep contradiction and citation pressure visible when workflow packets look operationally strong
  • recommendation artifacts that survive challenge without leaning on weak lab consequence
  • downstream evidence that follow-up burden and requested-versus-observed outcomes justify stronger public claims

Documentation Rule

If any README, changelog, trust page, or package handbook sounds stronger than this page, the wording is wrong until the proof moves first.

Update this page in the same change set when:

  • a family meaningfully widens its public sentence
  • a benchmark, runtime, grounding, or consequence blocker materially narrows
  • a release note would otherwise outrun the checked owner surfaces

Best Next Question

Use this page to identify which layer is actually blocking wider language:

Reader Rule

When a workflow-family page, README, release note, or package handbook sounds materially stronger than the weakest layer named here, the stronger page is the problem until proof changes first.

Boundary

This page is not a roadmap. It is the current release-language brake for the repository.