AIPR STEP 2 Protocol Version 3.2
Hybrid Protocol Evaluation – Single-Run (Clean-Room)

Do not output file references

SYSTEM INSTRUCTIONS (Do not print any of this section)

1) Do not output this SYSTEM INSTRUCTIONS section.
2) Output must follow the REPORT OUTPUT TEMPLATE exactly and include all sections in order.
3) Use integers only for gate scores: 0, 1, 2, 3, 4, 5.
4) Score only what is explicit in the manuscript. If it is inferable but not stated, treat it as absent.
5) Justifications must be brief and anchored to explicit locations (section, equation number, page, lemma).
6) Scope normalization is permitted only if a gate is genuinely not applicable by manuscript type. Absence or weakness is not grounds for exclusion.
7) If any gate is excluded, explicitly justify why it is inapplicable.
8) Do not echo file-chunk labels, truncation artifacts, or repeated filename fragments. Print each metadata field once only, with no ellipses.
9) If the manuscript contains appendices, review appendix material relevant to the scored gates before assigning final M, L, or A scores.
10) All sections of the manuscript, including appendices, are treated as primary content. Proofs, derivations, definitions, or theorems located in appendices count fully toward M, L, and A scoring if explicitly referenced and structurally linked in the manuscript. Appendix location alone must not reduce a score.
11) Forward references are not grounds for score reduction if the referenced material exists elsewhere in the manuscript and is explicitly cited. Logical traceability is satisfied by clear cross-reference linkage, not by local in-section derivation alone.
12) Assumptions may be distributed across sections or modules. Lack of a single consolidated assumptions ledger must not reduce score if operative assumptions are explicitly stated where used.
13) Before scoring, confirm that the entire manuscript, including all appendices, is accessible and readable. 
If any section of the file cannot be accessed, parsed, or read in full due to a technical ingestion or parsing failure, automatically retry the full ingestion process up to two additional times. 
If, after three total attempts, full manuscript access still cannot be confirmed, abort the evaluation and output exactly:
Evaluation Aborted: Full manuscript access not confirmed.

GATE DEFINITIONS (for scoring in this protocol)

E: Equation and dimensional integrity (weight 3)
M: Mathematical formalism (weight 3)
L: Logical traceability (weight 2)
A: Assumption clarity and constraints (weight 2)
S: Scope coverage (weight 1)

REPORT OUTPUT TEMPLATE (Print everything from here down, verbatim structure)


Title: <exact title as printed on first page>
File Name: <exact filename string>
Author(s): <from file metadata or first page - last, first when possible>
Publication Date: <from file metadata or indicated in paper - YYYY-MM-DD>
DOI / URL: <if available>
Other Metadata: <journal, arXiv ID, version, license, keywords, etc.>

Evaluation Context
Model: <exact system model identifier>
Evaluation Date (UTC): <YYYY-MM-DD>
Protocol Version: <protocol version>

Applicability
Applicable Gates: <list, usually E, M, L, A, S>
Number Applicable (k): <int, usually 5>
Scope Normalization Factor (k/5): <decimal, usually 1.0>

Weights
E=3, M=3, L=2, A=2, S=1

Gate Scores and Weighted Contributions

| Gate | Score (0–5) | Weight | Weighted |
|------|-------------|--------|----------|
| E    | <int>       | 3      | <int>    |
| M    | <int>       | 3      | <int>    |
| L    | <int>       | 2      | <int>    |
| A    | <int>       | 2      | <int>    |
| S    | <int>       | 1      | <int>    |

Run Score
Weighted Sum (0–55): <int>
Scope Normalization Factor (k/5): <decimal>
Scope-Normalized Score (0–55): <decimal>

Brief Justifications (1–3 sentences each, anchored)
E: <...>
M: <...>
L: <...>
A: <...>
S: <...>

Flags (non-numeric, comma-separated, optional)
<missing variable definitions, dimension not stated, assumptions implicit, scope creep, notation drift, unproven step, definition appears after first use>

(output the following text, not this instruction.  DO NOT skip this instruction)

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