--- before
+++ after
@@ -1,626 +0,0 @@
-import { SEQUENCE_VIEWER_LIMITS } from "../runtime-contract";
-import { expandNucleotideSymbol } from "../nucleotide-alphabet";
-import { getGeneticCode, translateGeneticCodeCodon } from "./genetic-code";
-import { reverseComplement, translateFrame } from "./translation";
-
-export type SequenceStatistics = {
-  ambiguousCount: number;
-  gcFraction: number | null;
-  length: number;
-  molecule: "nucleic-acid" | "protein";
-  nFraction: number | null;
-  symbolCounts: Record<string, number>;
-};
-
-export type SequenceOrf = {
-  aminoAcidLength: number;
-  completeStart: boolean;
-  completeStop: boolean;
-  end: number;
-  frame: 1 | 2 | 3 | -1 | -2 | -3;
-  geneticCodeId: number;
-  geneticCodeName: string;
-  nucleotideSequence: string;
-  start: number;
-  strand: "+" | "-";
-  translation: string;
-};
-
-export type RestrictionEnzyme = {
-  cutBottom: number;
-  cutTop: number;
-  id: string;
-  name: string;
-  recognitionSequence: string;
-};
-
-export type RestrictionSite = {
-  cutBottom: number;
-  cutTop: number;
-  end: number;
-  enzymeId: string;
-  enzymeName: string;
-  recognitionSequence: string;
-  start: number;
-  strand: "+" | "-";
-  wrapsOrigin: boolean;
-};
-
-export type DigestFragment = {
-  end: number;
-  length: number;
-  start: number;
-  wrapsOrigin: boolean;
-};
-
-export type PrimerCandidate = {
-  end: number;
-  gcFraction: number;
-  length: number;
-  score: number;
-  selfComplementarity: number;
-  sequence: string;
-  start: number;
-  strand: "+" | "-";
-  tmCelsius: number;
-};
-
-export type PrimerPair = {
-  forward: PrimerCandidate;
-  productEnd: number;
-  productLength: number;
-  productStart: number;
-  reverse: PrimerCandidate;
-  score: number;
-};
-
-export const COMMON_RESTRICTION_ENZYMES: ReadonlyArray<RestrictionEnzyme> =
-  Object.freeze([
-    enzyme("EcoRI", "GAATTC", 1, 5),
-    enzyme("BamHI", "GGATCC", 1, 5),
-    enzyme("HindIII", "AAGCTT", 1, 5),
-    enzyme("NotI", "GCGGCCGC", 2, 6),
-    enzyme("XhoI", "CTCGAG", 1, 5),
-    enzyme("XbaI", "TCTAGA", 1, 5),
-    enzyme("SpeI", "ACTAGT", 1, 5),
-    enzyme("NheI", "GCTAGC", 1, 5),
-    enzyme("PstI", "CTGCAG", 5, 1),
-    enzyme("KpnI", "GGTACC", 5, 1),
-    enzyme("SacI", "GAGCTC", 5, 1),
-    enzyme("SalI", "GTCGAC", 1, 5),
-    enzyme("SmaI", "CCCGGG", 3, 3),
-    enzyme("ApaI", "GGGCCC", 5, 1),
-    enzyme("BglII", "AGATCT", 1, 5),
-    enzyme("ClaI", "ATCGAT", 2, 4),
-    enzyme("DpnI", "GATC", 2, 2),
-    enzyme("HaeIII", "GGCC", 2, 2),
-    enzyme("MluI", "ACGCGT", 1, 5),
-    enzyme("NcoI", "CCATGG", 1, 5),
-    enzyme("NdeI", "CATATG", 2, 4),
-    enzyme("SbfI", "CCTGCAGG", 6, 2),
-    enzyme("BsaI", "GGTCTC", 7, 11),
-    enzyme("BsmBI", "CGTCTC", 7, 11),
-  ]);
-
-export function calculateSequenceStatistics(
-  sequence: string,
-  molecule: "nucleic-acid" | "protein",
-): SequenceStatistics {
-  const normalized = sequence.toUpperCase().replaceAll(/\s+/gu, "");
-  const symbolCounts: Record<string, number> = {};
-  for (const symbol of normalized) {
-    symbolCounts[symbol] = (symbolCounts[symbol] ?? 0) + 1;
-  }
-  if (molecule === "protein") {
-    const ambiguousCount = [...normalized].filter((symbol) =>
-      "BJOUXZ?".includes(symbol),
-    ).length;
-    return {
-      ambiguousCount,
-      gcFraction: null,
-      length: normalized.length,
-      molecule,
-      nFraction: null,
-      symbolCounts,
-    };
-  }
-  const canonicalCount =
-    (symbolCounts.A ?? 0) +
-    (symbolCounts.C ?? 0) +
-    (symbolCounts.G ?? 0) +
-    (symbolCounts.T ?? 0) +
-    (symbolCounts.U ?? 0);
-  const ambiguousCount = Math.max(0, normalized.length - canonicalCount);
-  return {
-    ambiguousCount,
-    gcFraction:
-      normalized.length === 0
-        ? 0
-        : ((symbolCounts.G ?? 0) + (symbolCounts.C ?? 0)) / normalized.length,
-    length: normalized.length,
-    molecule,
-    nFraction:
-      normalized.length === 0 ? 0 : (symbolCounts.N ?? 0) / normalized.length,
-    symbolCounts,
-  };
-}
-
-export function findOpenReadingFrames({
-  geneticCodeId = 1,
-  includePartial = false,
-  maxResults = SEQUENCE_VIEWER_LIMITS.analysis.maxOrfs,
-  minAminoAcids = 30,
-  sequence,
-  strands = "both",
-}: {
-  geneticCodeId?: number;
-  includePartial?: boolean;
-  maxResults?: number;
-  minAminoAcids?: number;
-  sequence: string;
-  strands?: "+" | "-" | "both";
-}): { items: Array<SequenceOrf>; truncated: boolean } {
-  const code = getGeneticCode(geneticCodeId);
-  if (code == null) {
-    throw new Error(`NCBI genetic code ${geneticCodeId} is not supported.`);
-  }
-  const normalized = normalizeDna(sequence);
-  const orientedSequences = [
-    ...(strands === "+" || strands === "both"
-      ? [{ sequence: normalized, strand: "+" as const }]
-      : []),
-    ...(strands === "-" || strands === "both"
-      ? [{ sequence: reverseComplement(normalized), strand: "-" as const }]
-      : []),
-  ];
-  const items: Array<SequenceOrf> = [];
-  let truncated = false;
-  for (const oriented of orientedSequences) {
-    for (let offset = 0; offset < 3; offset += 1) {
-      const openStarts: Array<number> = [];
-      for (
-        let index = offset;
-        index + 2 < oriented.sequence.length;
-        index += 3
-      ) {
-        const codon = oriented.sequence.slice(index, index + 3);
-        if (isUnambiguousStartCodon(codon, code.startCodons)) {
-          openStarts.push(index);
-        }
-        if (translateGeneticCodeCodon(codon, geneticCodeId) !== "*") continue;
-        for (const startIndex of openStarts) {
-          const aminoAcidLength = (index - startIndex) / 3;
-          if (aminoAcidLength < minAminoAcids) continue;
-          items.push(
-            createOrf({
-              completeStart: true,
-              completeStop: true,
-              endIndex: index + 3,
-              geneticCodeId,
-              geneticCodeName: code.name,
-              orientedSequence: oriented.sequence,
-              originalLength: normalized.length,
-              startIndex,
-              strand: oriented.strand,
-            }),
-          );
-          if (items.length >= maxResults) {
-            truncated = true;
-            return { items: sortOrfs(items), truncated };
-          }
-        }
-        openStarts.length = 0;
-      }
-      if (includePartial) {
-        for (const startIndex of openStarts) {
-          const endIndex =
-            oriented.sequence.length -
-            ((oriented.sequence.length - startIndex) % 3);
-          if ((endIndex - startIndex) / 3 < minAminoAcids) continue;
-          items.push(
-            createOrf({
-              completeStart: true,
-              completeStop: false,
-              endIndex,
-              geneticCodeId,
-              geneticCodeName: code.name,
-              orientedSequence: oriented.sequence,
-              originalLength: normalized.length,
-              startIndex,
-              strand: oriented.strand,
-            }),
-          );
-          if (items.length >= maxResults) {
-            truncated = true;
-            return { items: sortOrfs(items), truncated };
-          }
-        }
-      }
-    }
-  }
-  return { items: sortOrfs(items), truncated };
-}
-
-export function findRestrictionSites({
-  circular = false,
-  enzymes = COMMON_RESTRICTION_ENZYMES,
-  maxResults = SEQUENCE_VIEWER_LIMITS.analysis.maxRestrictionSites,
-  sequence,
-}: {
-  circular?: boolean;
-  enzymes?: ReadonlyArray<RestrictionEnzyme>;
-  maxResults?: number;
-  sequence: string;
-}): { items: Array<RestrictionSite>; truncated: boolean } {
-  const normalized = normalizeDna(sequence);
-  const items: Array<RestrictionSite> = [];
-  const seen = new Set<string>();
-  for (const enzymeDefinition of enzymes) {
-    const recognitionLength = enzymeDefinition.recognitionSequence.length;
-    const searchable = circular
-      ? normalized + normalized.slice(0, Math.max(0, recognitionLength - 1))
-      : normalized;
-    for (const strand of ["+", "-"] as const) {
-      const motif =
-        strand === "+"
-          ? enzymeDefinition.recognitionSequence
-          : reverseComplement(enzymeDefinition.recognitionSequence);
-      for (
-        let index = 0;
-        index + motif.length <= searchable.length;
-        index += 1
-      ) {
-        if (
-          index >= normalized.length ||
-          !matchesIupac(searchable.slice(index, index + motif.length), motif)
-        )
-          continue;
-        const start = index + 1;
-        const endUnwrapped = index + motif.length;
-        const wrapsOrigin = endUnwrapped > normalized.length;
-        const end = wrapsOrigin
-          ? endUnwrapped - normalized.length
-          : endUnwrapped;
-        const key = `${enzymeDefinition.id}:${start}:${end}`;
-        if (seen.has(key)) continue;
-        seen.add(key);
-        const cutBottom =
-          index +
-          (strand === "+"
-            ? enzymeDefinition.cutBottom
-            : recognitionLength - enzymeDefinition.cutTop) +
-          1;
-        const cutTop =
-          index +
-          (strand === "+"
-            ? enzymeDefinition.cutTop
-            : recognitionLength - enzymeDefinition.cutBottom) +
-          1;
-        items.push({
-          cutBottom: circular
-            ? wrapCoordinate(cutBottom, normalized.length)
-            : cutBottom,
-          cutTop: circular ? wrapCoordinate(cutTop, normalized.length) : cutTop,
-          end,
-          enzymeId: enzymeDefinition.id,
-          enzymeName: enzymeDefinition.name,
-          recognitionSequence: enzymeDefinition.recognitionSequence,
-          start,
-          strand,
-          wrapsOrigin,
-        });
-        if (items.length >= maxResults) return { items, truncated: true };
-      }
-    }
-  }
-  return {
-    items: items.sort(
-      (left, right) =>
-        left.start - right.start ||
-        left.enzymeName.localeCompare(right.enzymeName),
-    ),
-    truncated: false,
-  };
-}
-
-export function simulateDigest({
-  circular,
-  sequenceLength,
-  sites,
-}: {
-  circular: boolean;
-  sequenceLength: number;
-  sites: ReadonlyArray<RestrictionSite>;
-}): Array<DigestFragment> {
-  if (sequenceLength <= 0) return [];
-  const cuts = [
-    ...new Set(
-      sites.flatMap(({ cutTop }) => {
-        if (circular) return [wrapCoordinate(cutTop, sequenceLength)];
-        return cutTop >= 1 && cutTop <= sequenceLength ? [cutTop] : [];
-      }),
-    ),
-  ].sort((left, right) => left - right);
-  if (cuts.length === 0)
-    return [
-      {
-        end: sequenceLength,
-        length: sequenceLength,
-        start: 1,
-        wrapsOrigin: false,
-      },
-    ];
-  if (!circular) {
-    const boundaries = [1, ...cuts, sequenceLength + 1];
-    return boundaries.slice(0, -1).flatMap((start, index) => {
-      const next = boundaries[index + 1];
-      if (next == null || next <= start) return [];
-      return [
-        { end: next - 1, length: next - start, start, wrapsOrigin: false },
-      ];
-    });
-  }
-  return cuts.map((start, index) => {
-    const next = cuts[(index + 1) % cuts.length] ?? start;
-    const length = next > start ? next - start : sequenceLength - start + next;
-    return {
-      end: wrapCoordinate(start + length - 1, sequenceLength),
-      length,
-      start,
-      wrapsOrigin: next <= start,
-    };
-  });
-}
-
-export function designPrimerPairs({
-  maxPairs = 10,
-  maxPrimerLength = 25,
-  maxProductLength = 1_500,
-  minPrimerLength = 18,
-  minProductLength = 80,
-  optimumTm = 60,
-  sequence,
-  targetEnd,
-  targetStart,
-}: {
-  maxPairs?: number;
-  maxPrimerLength?: number;
-  maxProductLength?: number;
-  minPrimerLength?: number;
-  minProductLength?: number;
-  optimumTm?: number;
-  sequence: string;
-  targetEnd: number;
-  targetStart: number;
-}): Array<PrimerPair> {
-  const normalized = normalizeDna(sequence);
-  const boundedStart = Math.max(1, Math.min(targetStart, normalized.length));
-  const boundedEnd = Math.max(
-    boundedStart,
-    Math.min(targetEnd, normalized.length),
-  );
-  const forwardCandidates = enumeratePrimerCandidates({
-    maxPrimerLength,
-    minPrimerLength,
-    optimumTm,
-    sequence: normalized,
-    strand: "+",
-    windowEnd: Math.max(minPrimerLength, boundedStart),
-    windowStart: Math.max(1, boundedStart - 250),
-  });
-  const reverseCandidates = enumeratePrimerCandidates({
-    maxPrimerLength,
-    minPrimerLength,
-    optimumTm,
-    sequence: normalized,
-    strand: "-",
-    windowEnd: Math.min(normalized.length, boundedEnd + 250),
-    windowStart: Math.min(normalized.length, boundedEnd),
-  });
-  const pairs: Array<PrimerPair> = [];
-  for (const forward of forwardCandidates) {
-    for (const reverse of reverseCandidates) {
-      const productStart = forward.start;
-      const productEnd = reverse.end;
-      const productLength = productEnd - productStart + 1;
-      if (productLength < minProductLength || productLength > maxProductLength)
-        continue;
-      pairs.push({
-        forward,
-        productEnd,
-        productLength,
-        productStart,
-        reverse,
-        score:
-          forward.score +
-          reverse.score +
-          Math.abs(forward.tmCelsius - reverse.tmCelsius) * 2,
-      });
-      if (pairs.length >= SEQUENCE_VIEWER_LIMITS.analysis.maxPrimerCandidates)
-        break;
-    }
-    if (pairs.length >= SEQUENCE_VIEWER_LIMITS.analysis.maxPrimerCandidates)
-      break;
-  }
-  return pairs
-    .sort((left, right) => left.score - right.score)
-    .slice(0, maxPairs);
-}
-
-function enumeratePrimerCandidates({
-  maxPrimerLength,
-  minPrimerLength,
-  optimumTm,
-  sequence,
-  strand,
-  windowEnd,
-  windowStart,
-}: {
-  maxPrimerLength: number;
-  minPrimerLength: number;
-  optimumTm: number;
-  sequence: string;
-  strand: "+" | "-";
-  windowEnd: number;
-  windowStart: number;
-}): Array<PrimerCandidate> {
-  const candidates: Array<PrimerCandidate> = [];
-  for (let start = windowStart; start <= windowEnd; start += 1) {
-    for (let length = minPrimerLength; length <= maxPrimerLength; length += 1) {
-      const end = start + length - 1;
-      if (end > sequence.length || end > windowEnd) continue;
-      const genomic = sequence.slice(start - 1, end);
-      if (!/^[ACGT]+$/u.test(genomic)) continue;
-      const primerSequence =
-        strand === "+" ? genomic : reverseComplement(genomic);
-      const gcCount = [...primerSequence].filter(
-        (symbol) => symbol === "G" || symbol === "C",
-      ).length;
-      const gcFraction = gcCount / primerSequence.length;
-      if (gcFraction < 0.3 || gcFraction > 0.7) continue;
-      const tmCelsius = 2 * (primerSequence.length - gcCount) + 4 * gcCount;
-      const selfComplementarity = longestComplementaryRun(
-        primerSequence,
-        reverseComplement(primerSequence),
-      );
-      if (selfComplementarity >= 8) continue;
-      const homopolymerPenalty = /([ACGT])\1{4,}/u.test(primerSequence)
-        ? 10
-        : 0;
-      candidates.push({
-        end,
-        gcFraction,
-        length,
-        score:
-          Math.abs(tmCelsius - optimumTm) +
-          Math.abs(gcFraction - 0.5) * 20 +
-          selfComplementarity +
-          homopolymerPenalty,
-        selfComplementarity,
-        sequence: primerSequence,
-        start,
-        strand,
-        tmCelsius,
-      });
-      if (
-        candidates.length >= SEQUENCE_VIEWER_LIMITS.analysis.maxPrimerCandidates
-      )
-        return candidates;
-    }
-  }
-  return candidates
-    .sort((left, right) => left.score - right.score)
-    .slice(0, 100);
-}
-
-function createOrf({
-  completeStart,
-  completeStop,
-  endIndex,
-  geneticCodeId,
-  geneticCodeName,
-  orientedSequence,
-  originalLength,
-  startIndex,
-  strand,
-}: {
-  completeStart: boolean;
-  completeStop: boolean;
-  endIndex: number;
-  geneticCodeId: number;
-  geneticCodeName: string;
-  orientedSequence: string;
-  originalLength: number;
-  startIndex: number;
-  strand: "+" | "-";
-}): SequenceOrf {
-  const nucleotideSequence = orientedSequence.slice(startIndex, endIndex);
-  const rawTranslation = translateFrame(nucleotideSequence, 0, geneticCodeId);
-  const translation = rawTranslation.replace(/\*$/u, "");
-  const start = strand === "+" ? startIndex + 1 : originalLength - endIndex + 1;
-  const end = strand === "+" ? endIndex : originalLength - startIndex;
-  const offset = startIndex % 3;
-  return {
-    aminoAcidLength: translation.length,
-    completeStart,
-    completeStop,
-    end,
-    frame: (strand === "+"
-      ? offset + 1
-      : -(offset + 1)) as SequenceOrf["frame"],
-    geneticCodeId,
-    geneticCodeName,
-    nucleotideSequence,
-    start,
-    strand,
-    translation,
-  };
-}
-
-function sortOrfs(items: Array<SequenceOrf>): Array<SequenceOrf> {
-  return items.sort(
-    (left, right) =>
-      right.aminoAcidLength - left.aminoAcidLength || left.start - right.start,
-  );
-}
-
-function normalizeDna(sequence: string): string {
-  return sequence.toUpperCase().replaceAll("U", "T").replaceAll(/\s+/gu, "");
-}
-
-function isUnambiguousStartCodon(
-  codon: string,
-  startCodons: ReadonlySet<string>,
-): boolean {
-  if (/^[ACGT]{3}$/u.test(codon)) return startCodons.has(codon);
-  let candidates = [""];
-  for (const symbol of codon)
-    candidates = candidates.flatMap((prefix) =>
-      [...expandNucleotideSymbol(symbol)].map((base) => `${prefix}${base}`),
-    );
-  return (
-    candidates.length > 0 &&
-    candidates.every((candidate) => startCodons.has(candidate))
-  );
-}
-
-function matchesIupac(sequence: string, motif: string): boolean {
-  return [...motif].every((symbol, index) =>
-    expandNucleotideSymbol(symbol).has(sequence[index] ?? ""),
-  );
-}
-
-function wrapCoordinate(coordinate: number, length: number): number {
-  return length <= 0
-    ? coordinate
-    : ((((coordinate - 1) % length) + length) % length) + 1;
-}
-
-function longestComplementaryRun(left: string, right: string): number {
-  let longest = 0;
-  for (let offset = -right.length; offset <= left.length; offset += 1) {
-    let run = 0;
-    for (let index = 0; index < left.length; index += 1) {
-      if (left[index] === right[index - offset]) {
-        run += 1;
-        longest = Math.max(longest, run);
-      } else run = 0;
-    }
-  }
-  return longest;
-}
-
-function enzyme(
-  name: string,
-  recognitionSequence: string,
-  cutTop: number,
-  cutBottom: number,
-): RestrictionEnzyme {
-  return {
-    cutBottom,
-    cutTop,
-    id: name.toLowerCase(),
-    name,
-    recognitionSequence,
-  };
-}

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AFTER

Field is absent

removed `/files/src~1sequence~1pinned-inspector.tsx`

BEFORE

{
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AFTER

Field is absent

removed `/files/src~1sequence~1preview.test.tsx`

BEFORE

{
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AFTER

Field is absent

removed `/files/src~1sequence~1quality-track.tsx`

BEFORE

{
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AFTER

Field is absent

removed `/files/src~1sequence~1quality.ts`

BEFORE

{
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AFTER

Field is absent

removed `/files/src~1sequence~1read-pileup.test.ts`

BEFORE

{
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AFTER

Field is absent

removed `/files/src~1sequence~1read-pileup.ts`

BEFORE

{
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AFTER

Field is absent

removed `/files/src~1sequence~1record-list-panel.tsx`

BEFORE

{
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AFTER

Field is absent

removed `/files/src~1sequence~1search-panel.tsx`

BEFORE

{
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AFTER

Field is absent

removed `/files/src~1sequence~1search.test.ts`

BEFORE

{
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AFTER

Field is absent

removed `/files/src~1sequence~1search.ts`

BEFORE

{
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AFTER

Field is absent

removed `/files/src~1sequence~1selection.test.ts`

BEFORE

{
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AFTER

Field is absent

removed `/files/src~1sequence~1selection.ts`

BEFORE

{
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AFTER

Field is absent

removed `/files/src~1sequence~1sequence-legend.tsx`

BEFORE

{
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AFTER

Field is absent

removed `/files/src~1sequence~1sequence-line-layout.test.ts`

BEFORE

{
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AFTER

Field is absent

removed `/files/src~1sequence~1sequence-line-layout.ts`

BEFORE

{
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AFTER

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removed `/files/src~1sequence~1sequence-overview-geometry.ts`

BEFORE

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AFTER

Field is absent

removed `/files/src~1sequence~1sequence-overview.test.ts`

BEFORE

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AFTER

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removed `/files/src~1sequence~1sequence-overview.tsx`

BEFORE

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AFTER

Field is absent

removed `/files/src~1sequence~1sequence-palette.test.ts`

BEFORE

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AFTER

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removed `/files/src~1sequence~1sequence-palette.ts`

BEFORE

{
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AFTER

Field is absent

removed `/files/src~1sequence~1sequence-renderer.tsx`

BEFORE

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AFTER

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BEFORE

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AFTER

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BEFORE

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AFTER

Field is absent

removed `/files/src~1sequence~1sequence-workbench-panel.test.tsx`

BEFORE

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AFTER

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BEFORE

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AFTER

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BEFORE

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AFTER

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BEFORE

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AFTER

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BEFORE

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AFTER

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BEFORE

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AFTER

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BEFORE

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AFTER

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BEFORE

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AFTER

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BEFORE

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AFTER

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BEFORE

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AFTER

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BEFORE

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AFTER

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AFTER

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AFTER

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BEFORE

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AFTER

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BEFORE

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AFTER

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BEFORE

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AFTER

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AFTER

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AFTER

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AFTER

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AFTER

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AFTER

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AFTER

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AFTER

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AFTER

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AFTER

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AFTER

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AFTER

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AFTER

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AFTER

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AFTER

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BEFORE

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AFTER

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BEFORE

{
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AFTER

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BEFORE

{
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AFTER

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AFTER

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{
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AFTER

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BEFORE

{
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AFTER

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AFTER

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AFTER

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BEFORE

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AFTER

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{
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AFTER

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BEFORE

{
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AFTER

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BEFORE

{
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AFTER

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BEFORE

{
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AFTER

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BEFORE

{
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AFTER

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BEFORE

{
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AFTER

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BEFORE

{
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AFTER

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BEFORE

{
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AFTER

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BEFORE

{
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AFTER

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BEFORE

{
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AFTER

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BEFORE

{
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AFTER

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BEFORE

{
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AFTER

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BEFORE

{
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AFTER

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BEFORE

{
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AFTER

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BEFORE

{
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AFTER

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BEFORE

{
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AFTER

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BEFORE

{
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AFTER

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BEFORE

{
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AFTER

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BEFORE

{
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AFTER

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BEFORE

{
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AFTER

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BEFORE

{
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AFTER

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BEFORE

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AFTER

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BEFORE

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AFTER

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SHA-256 of public snapshot: 3d0564840f9fe2a4607dcfa3ac18b6f38a1415ca67c6b3f49ff495736b42f386

Update to Biological Sequence & Alignment Viewer

Package or technical metadata updated

Package file

Package file

Package file

Package file

Compare saved observations

Changed files

src/sequence/analysis.ts

changed /files/.codex-plugin~1plugin.json/sha256

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removed /files/e2e~1plugin-runtime-root.mjs

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added /files/integrity.json

added /files/launch_node

added /files/launch_node.cmd

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added `/files/integrity.json`

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