weavatrix 0.3.14 → 1.1.0

package/src/mcp/health/endpoints.mjs

@@ -1,71 +0,0 @@
-import {rawGraph} from '../graph-context.mjs'
-import {analyzeEndpointInventory} from '../../analysis/endpoints.js'
-import {PATH_CLASS_NAMES, createPathClassifier, hasPathClass} from '../../path-classification.js'
-import {toolResult} from '../tool-result.mjs'
-
-export function tListEndpoints(g, args, ctx) {
-    if (!ctx.repoRoot) return 'Endpoint detection needs the repo root (not provided to this server).'
-    const graph = rawGraph(ctx)
-    const codeFiles = [...new Set(
-        (graph.nodes || [])
-            .filter((n) => !String(n.id).includes('#') && n.source_file && n.file_type === 'code')
-            .map((n) => n.source_file)
-    )]
-    const inventory = analyzeEndpointInventory(ctx.repoRoot, codeFiles)
-    let eps = inventory.endpoints
-    const method = args.method ? String(args.method).toUpperCase() : null
-    const path = args.path ? String(args.path) : null
-    if (method) eps = eps.filter((endpoint) => endpoint.method === method)
-    if (path) eps = eps.filter((endpoint) => endpoint.path === path || endpoint.path.endsWith(path))
-    // Production-first: classified endpoints are suppressed by default; a tests-only graph would
-    // suppress everything, so that build mode auto-includes them (same precedent as module_map).
-    const includeClassified = args.include_classified === true || graph.graphBuildMode === 'tests-only'
-    const classifier = createPathClassifier(ctx.repoRoot)
-    const byFile = new Map()
-    const classesOf = (file) => {
-        const key = String(file || '')
-        if (!byFile.has(key)) {
-            const info = classifier.explain(key, {content: ''})
-            byFile.set(key, {classified: info.excluded || hasPathClass(info, ...PATH_CLASS_NAMES), pathClasses: info.classes})
-        }
-        return byFile.get(key)
-    }
-    const production = eps.filter((endpoint) => !classesOf(endpoint.file).classified)
-    const classified = eps.filter((endpoint) => classesOf(endpoint.file).classified)
-    const suppressed = includeClassified ? 0 : classified.length
-    eps = includeClassified ? [...production, ...classified] : production
-    const suppressionNote = suppressed
-        ? `${suppressed} endpoint(s) in classified test/e2e/generated/vendored/mock/story/docs/benchmark/temp or explicitly excluded paths were suppressed; pass include_classified:true to inspect them.`
-        : ''
-    if (!eps.length) return suppressed
-        ? `No production HTTP endpoints detected; ${suppressionNote}`
-        : 'No HTTP endpoints detected in the indexed code files.'
-    const max = Math.max(1, Math.min(300, Number(args.max_results) || 100))
-    const shown = eps.slice(0, max)
-    const stats = inventory.stats
-    const text = [
-        `${eps.length} endpoint(s) matched${eps.length > shown.length ? `, showing ${shown.length}` : ''}. Inventory: ${stats.declaredRoutes} declaration(s); ${stats.reachableStaticRoutes} statically reachable composed route(s); ${stats.localDeclarations} local/root declaration candidate(s); ${stats.staticMounts} static router mount(s)${stats.truncated ? `; TRUNCATED at ${stats.maxEndpoints}` : ''}.${suppressed ? ` ${suppressionNote}` : ''}`,
-        ...shown.map((e) => {
-            const via = e.mountChain?.length
-                ? `\n           declared ${e.declaredPath} in ${e.file}${e.line ? `:${e.line}` : ''}; mount chain ${e.mountChain.map((mount) => `${mount.file}:${mount.line} ${mount.path}`).join(' → ')}`
-                : ''
-            const activation = e.conditional
-                ? `; conditional default ${e.defaultActive === false ? 'inactive' : e.defaultActive === true ? 'active' : 'unknown'}`
-                : ''
-            const info = classesOf(e.file)
-            const tag = info.classified ? ` [classified${info.pathClasses.length ? `:${info.pathClasses.join('+')}` : ''}]` : ''
-            return `  ${e.method.toUpperCase().padEnd(6)} ${e.path}${e.handler ? `  → ${e.handler}` : ''}  (${e.file}${e.line ? `:${e.line}` : ''}; ${e.mountState}/${e.confidence}${activation})${tag}${via}`
-        }),
-    ].join('\n')
-    return toolResult(text, {
-        filters: {method, path},
-        stats,
-        pathPolicy: includeClassified ? 'all' : 'production-first',
-        suppressed,
-        endpoints: shown.map((e) => {
-            const info = classesOf(e.file)
-            return info.classified ? {...e, classified: true, pathClasses: info.pathClasses} : e
-        }),
-        page: {shown: shown.length, total: eps.length, truncated: eps.length > shown.length || stats.truncated},
-    }, {completeness: {status: stats.truncated ? 'PARTIAL' : 'COMPLETE', reason: stats.truncated ? `endpoint cap ${stats.maxEndpoints} reached` : 'all indexed code files scanned'}})
-}

package/src/mcp/health/structure.mjs

@@ -1,220 +0,0 @@
-import {degreeOf, rawGraph} from '../graph-context.mjs'
-import {summarizeCommunities, aggregateGraph} from '../../analysis/graph-analysis.js'
-import {computeStaticTestReachability} from '../../analysis/static-test-reachability.js'
-import {computeHotPathReview} from '../../analysis/hot-path-review.js'
-import {createPathClassifier, hasPathClass} from '../../path-classification.js'
-import {toolResult} from '../tool-result.mjs'
-
-export function tListCommunities(g, args, ctx) {
-    const max = Math.max(1, Math.min(100, Number(args.top_n) || 20))
-    const list = summarizeCommunities(ctx.graphPath, max)
-    if (!list.length) return 'No communities found in the graph.'
-    return [
-        `Communities, largest first (list position = community_id for get_community):`,
-        ...list.map((c, i) => `${String(i).padStart(3)}. ${c.name} — ${c.size} nodes (raw id ${c.id}; e.g. ${[...new Set(c.files)].join(', ')})`),
-    ].join('\n')
-}
-
-// Folder-level architecture map: modules (top-two path segments) with file/symbol counts and the
-// strongest module→module dependencies. Pure graph aggregation — no filesystem reads.
-export function tModuleMap(g, args, ctx) {
-    const graph = rawGraph(ctx)
-    const testsOnly = graph.graphBuildMode === 'tests-only'
-    const includeNonProduct = args.include_non_product === true || testsOnly
-    const classifier = createPathClassifier(ctx?.repoRoot || null)
-    const nonProductFiles = new Set()
-    const classifiedFiles = new Set()
-    if (!includeNonProduct) {
-        for (const node of graph.nodes || []) {
-            if (!node?.source_file) continue
-            const sourceFile = String(node.source_file)
-            if (classifiedFiles.has(sourceFile)) continue
-            classifiedFiles.add(sourceFile)
-            const explanation = classifier.explain(sourceFile)
-            if (explanation.excluded || hasPathClass(explanation, 'test', 'e2e', 'generated', 'vendored', 'mock', 'story', 'docs', 'benchmark', 'temp')) {
-                nonProductFiles.add(sourceFile)
-            }
-        }
-    }
-    const visibleGraph = includeNonProduct || nonProductFiles.size === 0 ? graph : (() => {
-        const keep = new Set((graph.nodes || [])
-            .filter((node) => !node?.source_file || !nonProductFiles.has(String(node.source_file)))
-            .map((node) => String(node.id)))
-        const endpoint = (value) => String(value && typeof value === 'object' ? value.id : value)
-        return {
-            ...graph,
-            nodes: (graph.nodes || []).filter((node) => keep.has(String(node.id))),
-            links: (graph.links || []).filter((link) => keep.has(endpoint(link.source)) && keep.has(endpoint(link.target))),
-        }
-    })()
-    const agg = aggregateGraph(visibleGraph, null)
-    const topN = Math.max(1, Math.min(60, Number(args.top_n) || 25))
-    const mods = agg.modules.slice(0, topN)
-    const edges = agg.moduleEdges.slice(0, Math.min(50, topN * 2))
-    const compileEdges = new Map()
-    const collectCompileEdges = (list, kind) => {
-        for (const edge of list || []) {
-            const key = `${edge.from}\0${edge.to}`
-            const current = compileEdges.get(key) || {from: edge.from, to: edge.to, count: 0, typeOnly: 0, compileOnly: 0}
-            current.count += edge.count
-            current[kind] += edge.count
-            compileEdges.set(key, current)
-        }
-    }
-    collectCompileEdges(agg.typeOnlyModuleEdges, 'typeOnly')
-    collectCompileEdges(agg.compileOnlyModuleEdges, 'compileOnly')
-    const compiled = [...compileEdges.values()].sort((a, b) => b.count - a.count).slice(0, Math.min(50, topN * 2))
-    return [
-        testsOnly
-            ? 'Scope: tests-only graph; classified test/e2e/fixture surfaces are retained automatically.'
-            : includeNonProduct
-            ? 'Scope: all indexed files, including classified non-product surfaces.'
-            : `Scope: production-only (default); excluded ${nonProductFiles.size} classified test/fixture/benchmark/generated/docs file(s). Pass include_non_product:true for the complete graph.`,
-        `Module map: ${agg.totals.files} files in ${agg.modules.length} folder-modules, ${agg.totals.moduleEdges} runtime module dependencies and ${agg.totals.compileTimeModuleEdges || 0} compile-time dependencies (${agg.totals.typeOnlyModuleEdges || 0} type-only, ${agg.totals.compileOnlyModuleEdges || 0} compile-only). Top ${mods.length}:`,
-        ...mods.map((m) => `  ${m.name} — ${m.fileCount} files, ${m.symbolCount} symbols`),
-        ``,
-        `Strongest runtime module dependencies:`,
-        ...edges.map((e) => `  ${e.from} → ${e.to}  (${e.count})`),
-        compiled.length ? `` : null,
-        compiled.length ? `Compile-time module dependencies (not runtime coupling):` : null,
-        ...compiled.map((e) => `  ${e.from} → ${e.to}  (${e.count}; ${e.typeOnly} type-only, ${e.compileOnly} compile-only)`),
-    ].filter((line) => line != null).join('\n')
-}
-
-// Parser-backed local cost review. This keeps syntax, graph coupling and measured/static test
-// evidence as separate fields so callers cannot mistake a ranking heuristic for profiler output.
-export function tHotPathReview(g, args, ctx) {
-    const review = computeHotPathReview(rawGraph(ctx), {
-        repoRoot: ctx?.repoRoot || null,
-        path: args.path,
-        includeTests: args.include_tests === true,
-        includeClassified: args.include_classified === true,
-        topN: args.top_n,
-        cyclomaticThreshold: args.cyclomatic_threshold,
-        callThreshold: args.call_threshold,
-        loopDepthThreshold: args.loop_depth_threshold,
-        timeRankThreshold: args.time_rank_threshold,
-        minScore: args.min_score,
-    })
-    if (!review.ok) return toolResult(`Hot-path review refused: ${review.error}.`, review)
-    const pct = (value) => typeof value === 'number' ? `${Math.round(value * 100)}%` : String(value || 'NOT_AVAILABLE')
-    const coverageLine = review.coverage.actualCoverage === 'AVAILABLE'
-        ? `Measured coverage: ${review.coverage.measuredFiles} file(s) from ${review.coverage.sources.join(', ') || 'coverage report'}.`
-        : review.coverage.staticReachability
-            ? `actualCoverage: NOT_AVAILABLE; static test reachability ${review.coverage.staticReachability.reachableFiles}/${review.coverage.staticReachability.productFiles} product file(s).`
-            : 'actualCoverage: NOT_AVAILABLE; no measured or static test evidence was available.'
-    const text = [
-        `Local hot-path review: ${review.candidateSymbols} candidate(s) from ${review.analyzedSymbols} analyzed symbol(s); showing ${review.hotspots.length}.`,
-        `Thresholds: time rank >=${review.thresholds.timeRank}, cyclomatic >=${review.thresholds.cyclomatic}, calls >=${review.thresholds.calls}, loop depth >=${review.thresholds.loopDepth}, score >=${review.thresholds.minScore}.`,
-        `Selection: ${review.selectionPolicy.mode}${review.selectionPolicy.strongLocalFallback ? '; strong local sort/recursion/deep-loop evidence can pass below the blended score gate' : '; strict explicit score gate'}.`,
-        coverageLine,
-        'Local syntax cost and graph coupling are separate. Scores are review priority, not measured runtime.',
-        '',
-        ...(review.hotspots.length ? review.hotspots.flatMap((item, index) => {
-            const tests = item.testEvidence.actualCoverage === 'NOT_AVAILABLE'
-                ? item.testEvidence.staticReachable ? `static-test d${item.testEvidence.distance}` : 'no-static-test-path'
-                : `coverage ${pct(item.testEvidence.actualCoverage)}`
-            const pointer = `${item.file}${item.startLine ? `:${item.startLine}${item.endLine > item.startLine ? `-${item.endLine}` : ''}` : ''}`
-            const evidence = item.sourceEvidence.length
-                ? `\n       evidence: ${item.sourceEvidence.map((entry) => `${entry.kind}@L${entry.line || '?'}${entry.detail ? ` (${entry.detail})` : ''}`).join('; ')}`
-                : ''
-            return [
-                `  ${String(index + 1).padStart(2)}. score ${String(item.score).padStart(5)}  syntax ${String(item.localSyntax.score).padStart(5)}  graph ${String(item.graphRisk.score).padStart(5)}  ${item.confidence}`,
-                `      ${item.label}  (${pointer}; fan-in ${item.graphRisk.fanIn}, fan-out ${item.graphRisk.fanOut}; ${tests})`,
-                `       ${item.reasons.slice(0, 5).join('; ')}${evidence}`,
-            ]
-        }) : ['  (none at the selected thresholds)']),
-        review.bounds.truncated ? `... +${review.bounds.totalCandidates - review.bounds.returned} more (raise top_n to display more, raise min_score or narrow path to tighten; lower min_score to broaden).` : null,
-        '',
-        'Caveat: no interprocedural Big-O, recursion-bound, CFG, dead-store or taint-flow claim is made.',
-    ].filter((line) => line != null).join('\n')
-    return toolResult(text, review, {
-        completeness: {
-            symbols: 'COMPLETE_FOR_INDEXED_GRAPH',
-            output: review.bounds.truncated ? 'BOUNDED' : 'COMPLETE',
-            coverage: review.coverage.actualCoverage,
-        },
-    })
-}
-
-// Coverage × graph: map an EXISTING coverage report (istanbul/lcov/coverage.py/Go — read offline,
-// tests are never executed here) onto files and symbols, then rank refactor risk as
-// connectivity × uncovered share. Pairs with get_dependents: many dependents + low coverage ⇒ write
-// tests before changing. Coverage pcts in this layer are fractions (0..1).
-export function tCoverageMap(g, args, ctx) {
-    if (!ctx.repoRoot) return 'Coverage mapping needs the repo root (not provided to this server).'
-    const agg = aggregateGraph(rawGraph(ctx), ctx.repoRoot)
-    const pathFilter = args.path ? String(args.path).replace(/\\/g, '/').replace(/\/+$/, '') : null
-    const inScope = (p) => !pathFilter || p === pathFilter || String(p).startsWith(`${pathFilter}/`)
-    const allFiles = agg.modules.flatMap((m) => m.files.filter((f) => inScope(f.path)))
-    const measured = allFiles.filter((f) => f.coverage != null)
-    if (!measured.length) {
-        const fallback = computeStaticTestReachability(rawGraph(ctx), {repoRoot: ctx.repoRoot, path: pathFilter || ''})
-        const topN = Math.max(1, Math.min(50, Number(args.top_n) || 15))
-        const reachable = fallback.reachable.slice(0, topN)
-        const unreachable = fallback.unreachable.slice(0, topN)
-        return [
-            `Static test reachability${pathFilter ? ` for ${pathFilter}` : ''}: ${fallback.reachableFiles}/${fallback.productFiles} product file(s) have a runtime graph path from ${fallback.testFiles} indexed test file(s).`,
-            `actualCoverage: ${fallback.actualCoverage}. This is NOT coverage: imports/calls only show that a test can statically reach a file, never that a line, branch or symbol executed.`,
-            fallback.bounds.truncated ? `Traversal was bounded/truncated (${fallback.bounds.traversedStates}/${fallback.bounds.maxStates} states, depth ≤${fallback.bounds.maxDepth}, ${fallback.testFiles}/${fallback.totalTestFiles} test files).` : `Traversal: ${fallback.bounds.traversedStates} bounded state(s), depth ≤${fallback.bounds.maxDepth}.`,
-            '',
-            'Nearest runtime paths from tests:',
-            ...(reachable.length ? reachable.map((entry) => {
-                const nearest = entry.nearestTests[0]
-                return `  ${nearest.confidence.padStart(6)}  d${nearest.distance}  ${entry.file}  ← ${nearest.test}\n          path: ${nearest.path.join(' → ')}`
-            }) : ['  (none)']),
-            '',
-            `No runtime path from an indexed test (${fallback.unreachableFiles}; not proof of no tests):`,
-            ...(unreachable.length ? unreachable.map((file) => `  ${file}`) : ['  (none)']),
-            fallback.unreachableFiles > unreachable.length ? `  … +${fallback.unreachableFiles - unreachable.length} more (raise top_n or narrow path)` : null,
-            '',
-            'No coverage report found — generate one for measured coverage:',
-            'Generate one with the repo\'s own test runner, then call coverage_map again:',
-            '  JS/TS:  npx vitest run --coverage   (or jest --coverage)',
-            '  Python: pytest --cov --cov-report=json',
-            '  Go:     go test ./... -coverprofile=coverage.out',
-            '  Rust:   cargo tarpaulin --out Json --output-dir .',
-            '          or cargo llvm-cov --lcov --output-path lcov.info',
-            'Read locations: coverage/coverage-summary.json, coverage/coverage-final.json, (coverage/)lcov.info, coverage.json, tarpaulin-report.json, coverage.out.',
-        ].filter((line) => line != null).join('\n')
-    }
-    const pctStr = (v) => (v == null ? 'n/a' : `${Math.round(v * 100)}%`)
-    const sources = [...new Set(measured.map((f) => f.coverageSource).filter(Boolean))]
-    const avg = measured.reduce((s, f) => s + f.coverage, 0) / measured.length
-    const rollup = agg.modules
-        .map((m) => {
-            const withCov = m.files.filter((f) => f.coverage != null && inScope(f.path))
-            if (!withCov.length) return null
-            return {
-                name: m.name,
-                measured: withCov.length,
-                total: m.files.filter((f) => inScope(f.path)).length,
-                avg: withCov.reduce((s, f) => s + f.coverage, 0) / withCov.length,
-            }
-        })
-        .filter(Boolean)
-        .sort((a, b) => a.avg - b.avg)
-    const topN = Math.max(1, Math.min(50, Number(args.top_n) || 15))
-    // risk = graph degree × uncovered share; only symbols below 80% matter
-    const risky = agg.symbols
-        .filter((s) => s.coverage != null && s.coverage < 0.8 && inScope(s.file))
-        .map((s) => ({...s, degree: degreeOf(g, s.id)}))
-        .filter((s) => s.degree > 0)
-        .sort((a, b) => b.degree * (1 - b.coverage) - a.degree * (1 - a.coverage))
-        .slice(0, topN)
-    return [
-        `Coverage map (${measured.length}/${allFiles.length} files measured, avg ${pctStr(avg)}; report: ${sources.join(', ') || 'unknown'}${pathFilter ? `; filter ${pathFilter}` : ''}).`,
-        ``,
-        `Modules by average coverage (worst first):`,
-        ...rollup.slice(0, 20).map((m) => `  ${pctStr(m.avg).padStart(5)}  ${m.name}  (${m.measured}/${m.total} files measured)`),
-        ``,
-        `Refactor-risk hotspots — connected symbols with low coverage (ranked by degree × uncovered):`,
-        ...(risky.length
-            ? risky.map((s) => `  ${pctStr(s.coverage).padStart(5)}  deg ${String(s.degree).padStart(3)}  ${s.label}  (${s.file}${s.line ? `:${s.line}` : ''})`)
-            : ['  (none — every connected symbol is ≥80% covered or unmeasured)']),
-        ``,
-        `Tip: before refactoring a hotspot, run get_dependents on it — low coverage × many dependents means write tests first.`,
-    ].join('\n')
-}
-
-// HTTP endpoint inventory: Express/Fastify/Nest/Flask/FastAPI/Go/Rust/Spring route definitions.

package/src/mcp/runtime-version.mjs

@@ -1,31 +0,0 @@
-import {readFileSync} from 'node:fs'
-import process from 'node:process'
-
-const STALE_RUNTIME_OVERRIDE_ENV = 'WEAVATRIX_ALLOW_STALE_RUNTIME'
-
-export function runtimeVersionStatus({runningVersion, packageJsonPath, allowStale} = {}) {
-    let diskVersion = null, packageVersionError = null
-    try {
-        const parsed = JSON.parse(readFileSync(packageJsonPath, 'utf8'))
-        diskVersion = typeof parsed?.version === 'string' && parsed.version.trim() ? parsed.version.trim() : null
-        if (!diskVersion) packageVersionError = 'package.json has no valid version'
-    } catch (error) {
-        packageVersionError = `package.json is unreadable: ${error.message}`
-    }
-    const staleRuntime = diskVersion !== String(runningVersion || '')
-    const staleRuntimeAllowed = allowStale == null
-        ? process.env[STALE_RUNTIME_OVERRIDE_ENV] === '1'
-        : allowStale === true
-    return {
-        version: String(runningVersion || ''),
-        diskVersion,
-        staleRuntime,
-        staleRuntimeAllowed,
-        ...(packageVersionError ? {packageVersionError} : {}),
-    }
-}
-
-export function staleRuntimeMessage(status) {
-    const disk = status.diskVersion || 'unavailable'
-    return `STALE_RUNTIME: running Weavatrix ${status.version || 'unknown'} but package.json on disk is ${disk}. Restart/reconnect the MCP server before using tools. For deliberate source-development only, set ${STALE_RUNTIME_OVERRIDE_ENV}=1.`
-}

package/src/mcp/server/auto-refresh.mjs

@@ -1,66 +0,0 @@
-import {dirname} from 'node:path'
-import {buildGraphForRepo, defaultPrecisionMode} from '../../build-graph.js'
-import {persistedFreshnessMatches, repositoryFreshnessProbe} from '../../graph/freshness-probe.js'
-import {PRECISION_OVERLAY_V, precisionSemanticInputsMatch, readPrecisionOverlay} from '../../precision/lsp-overlay.js'
-import {loadGraph} from '../graph-context.mjs'
-
-export function createAutoRefresh(getApi) {
-    const probeCache = new Map()
-    const configured = process.env.WEAVATRIX_AUTO_REFRESH_DEBOUNCE_MS == null
-        ? 2_000 : Number(process.env.WEAVATRIX_AUTO_REFRESH_DEBOUNCE_MS)
-    const debounceMs = Math.max(0, Math.min(5_000, Number.isFinite(configured) ? configured : 2_000))
-    return async function autoRefresh(callCtx, currentGraph) {
-        if (!callCtx?.repoRoot || !callCtx?.graphPath) return {graph: null, refresh: null}
-        const activePrecision = currentGraph?.graphPrecisionMode || defaultPrecisionMode()
-        const probeKey = `${callCtx.graphPath}\0${currentGraph?.graphBuildMode || 'full'}\0${activePrecision}`
-        let semanticInputsChanged = false
-        if (activePrecision === 'lsp' && currentGraph) {
-            try {
-                const overlay = readPrecisionOverlay(callCtx.graphPath, currentGraph)
-                semanticInputsChanged = typeof overlay?.semanticInputFingerprint === 'string'
-                    && !precisionSemanticInputsMatch(overlay, callCtx.repoRoot, currentGraph)
-            } catch {
-                semanticInputsChanged = true
-            }
-        }
-        const cached = probeCache.get(probeKey)
-        if (!semanticInputsChanged && currentGraph && cached && Date.now() - cached.checkedAt < debounceMs) {
-            return {graph: currentGraph, refresh: {kind: 'none', revision: currentGraph.graphRevision || null, changedFiles: 0}}
-        }
-        const beforeProbe = repositoryFreshnessProbe(callCtx.repoRoot)
-        const precisionMissing = activePrecision === 'lsp' && (
-            Number(currentGraph?.precisionOverlayV) !== PRECISION_OVERLAY_V || semanticInputsChanged
-        )
-        if (!precisionMissing && beforeProbe && currentGraph && (
-            cached?.probe === beforeProbe
-            || persistedFreshnessMatches(currentGraph, beforeProbe, currentGraph.graphBuildMode || 'full')
-        )) {
-            probeCache.set(probeKey, {probe: beforeProbe, checkedAt: Date.now()})
-            return {graph: currentGraph, refresh: {kind: 'none', revision: currentGraph.graphRevision || null, changedFiles: 0}}
-        }
-        const result = await buildGraphForRepo(callCtx.repoRoot, {
-            mode: currentGraph?.graphBuildMode || 'full',
-            precision: activePrecision,
-            scope: '',
-            outDir: dirname(callCtx.graphPath),
-        })
-        if (!result.ok) throw new Error(result.error || 'automatic graph refresh failed')
-        getApi().resetStalenessCache()
-        const fresh = loadGraph(callCtx.graphPath, {repoRoot: callCtx.repoRoot})
-        const afterProbe = repositoryFreshnessProbe(callCtx.repoRoot)
-        if (afterProbe && afterProbe === beforeProbe) probeCache.set(probeKey, {probe: afterProbe, checkedAt: Date.now()})
-        else probeCache.delete(probeKey)
-        const update = result.refresh || {kind: 'full', changedFiles: [], reason: 'automatic-refresh'}
-        return {
-            graph: fresh,
-            refresh: {
-                kind: update.kind,
-                revision: update.revision || fresh.graphRevision || null,
-                changedFiles: Array.isArray(update.changedFiles) ? update.changedFiles.length : 0,
-                notice: update.kind === 'none'
-                    ? undefined
-                    : `Graph ${update.kind === 'incremental' ? 'incrementally refreshed' : 'rebuilt'} before this answer (${update.reason || 'repository changed'}).`,
-            },
-        }
-    }
-}

package/src/mcp/server/runtime-config.mjs

@@ -1,43 +0,0 @@
-import {createRequire} from 'node:module'
-import {existsSync, realpathSync, statSync} from 'node:fs'
-import {dirname, join} from 'node:path'
-import {fileURLToPath} from 'node:url'
-import {graphOutDirForRepo} from '../../graph/layout.js'
-
-const SOURCE_DIR = join(dirname(fileURLToPath(import.meta.url)), '..', '..')
-const MCP_DIR = join(SOURCE_DIR, 'mcp')
-const CATALOG_URL = new URL('../catalog.mjs', import.meta.url)
-
-export const PACKAGE_JSON_PATH = join(SOURCE_DIR, '..', 'package.json')
-export const PACKAGE_VERSION = (() => {
-    try { return createRequire(import.meta.url)('../../../package.json').version } catch { return '0.0.0' }
-})()
-export const SERVER_INFO = {name: 'weavatrix', version: PACKAGE_VERSION}
-
-export const loadServerCatalog = (version = 0) => import(version ? `${CATALOG_URL.href}?v=${version}` : CATALOG_URL.href)
-
-export function hotCatalogVersion(hotFiles) {
-    let version = 0
-    for (const file of hotFiles) {
-        try {
-            const modified = statSync(join(MCP_DIR, file)).mtimeMs
-            if (modified > version) version = modified
-        } catch { /* a missing file does not bump the version */ }
-    }
-    return version
-}
-
-export function resolveServerTarget(argv, log = () => {}) {
-    let graphPath = argv[2], repoArg = argv[3], capabilities = argv[4]
-    try {
-        if (graphPath && statSync(graphPath).isDirectory()) {
-            repoArg = realpathSync.native(graphPath)
-            capabilities = argv[3]
-            graphPath = join(graphOutDirForRepo(repoArg), 'graph.json')
-            if (!existsSync(graphPath)) log(`no graph built yet for ${repoArg} — ask the agent to call rebuild_graph; it builds into the standard weavatrix-graphs layout`)
-        }
-    } catch { /* argv[2] is a graph path or unavailable */ }
-    let repoRoot = null
-    try { if (repoArg && statSync(repoArg).isDirectory()) repoRoot = realpathSync.native(repoArg) } catch { /* invalid repo root */ }
-    return {graphPath, repoRoot, capabilities}
-}

package/src/mcp/server/shutdown.mjs

@@ -1,40 +0,0 @@
-import process from 'node:process'
-import {
-    activeLspClientCount,
-    beginLspClientShutdown,
-    shutdownActiveLspClients,
-} from '../../precision/lsp-client.js'
-
-async function settleWithin(promise, timeoutMs) {
-    let timer
-    const settled = await Promise.race([
-        Promise.resolve(promise).then(() => true, () => true),
-        new Promise((resolve) => { timer = setTimeout(() => resolve(false), timeoutMs) }),
-    ])
-    if (timer) clearTimeout(timer)
-    return settled
-}
-
-export function createShutdownController({log, targetMutation}) {
-    let shuttingDown = false, shutdownPromise = null
-    const request = (reason, exitCode = 0) => {
-        if (shutdownPromise) return shutdownPromise
-        shuttingDown = true
-        beginLspClientShutdown()
-        process.stdin.pause()
-        const activeAtStart = activeLspClientCount()
-        log(`shutdown requested (${reason}); draining graph work and ${activeAtStart} semantic provider(s)`)
-        shutdownPromise = (async () => {
-            const initiallyDrained = await settleWithin(targetMutation(), 2_500)
-            const semantic = await shutdownActiveLspClients({timeoutMs: 3_000})
-            const fullyDrained = initiallyDrained || await settleWithin(targetMutation(), 1_500)
-            log(`shutdown cleanup: graph=${fullyDrained ? 'drained' : 'bounded-timeout'}, semantic=${semantic.requested} requested/${semantic.remaining} remaining${semantic.timedOut ? ' (forced)' : ''}`)
-        })().catch((error) => {
-            log(`shutdown cleanup failed: ${error.stack || error.message}`)
-        }).finally(() => {
-            process.exit(exitCode)
-        })
-        return shutdownPromise
-    }
-    return {isShuttingDown: () => shuttingDown, request}
-}

package/src/mcp/staleness-notice.mjs

@@ -1,20 +0,0 @@
-// Staleness is important, but repeating an identical paragraph after every graph call drowns the
-// actual answer. Surface a changed condition immediately, then remind periodically. graph_stats can
-// force the notice because freshness is the purpose of that tool.
-export function createStalenessNoticeGate(cooldownMs = 5 * 60_000) {
-    let lastKey = ''
-    let lastShownAt = 0
-    return {
-        shouldShow({line, graphPath = '', force = false, now = Date.now()} = {}) {
-            if (!line) return false
-            const key = `${graphPath}\u0000${line}`
-            if (force || key !== lastKey || now - lastShownAt >= cooldownMs) {
-                lastKey = key
-                lastShownAt = now
-                return true
-            }
-            return false
-        },
-        reset() { lastKey = ''; lastShownAt = 0 },
-    }
-}

package/src/mcp/sync/evidence-architecture.mjs

@@ -1,54 +0,0 @@
-import {
-    CAPS, SEVERITIES, bool, compare, count, int, list, moduleId, path,
-    reasons, state, text, token, verdict,
-} from './evidence-common.mjs'
-
-function moduleFact(value) {
-    const id = moduleId(value?.id || value?.name)
-    return id ? {id, fileCount: int(value.fileCount), nodeCount: int(value.nodeCount), symbolCount: int(value.symbolCount)} : null
-}
-
-function dependency(value) {
-    const from = moduleId(value?.from), to = moduleId(value?.to)
-    return from && to && from !== to ? {from, to, count: int(value.count)} : null
-}
-
-function cycleFact(value) {
-    const id = text(value?.id, 64), kind = value?.kind
-    if (!id || !/^[a-f0-9]{16,64}$/i.test(id) || !['runtime', 'compile-time'].includes(kind)) return null
-    const members = [...new Set((value.members || []).map((item) => path(item)).filter(Boolean))].sort(compare).slice(0, 200)
-    const representativePath = (value.representativePath || []).map((item) => path(item)).filter(Boolean).slice(0, 201)
-    if (members.length < 2 || representativePath.length < 2) return null
-    return {id, kind, size: Math.max(int(value.size), members.length), members, membersTruncated: bool(value.membersTruncated) || int(value.size) > members.length, representativePath}
-}
-
-function boundaryFact(value) {
-    const ruleId = token(value?.ruleId, 96), from = path(value?.from), to = path(value?.to)
-    if (!ruleId || !from || !to || !['forbidden', 'allowedOnly'].includes(value?.kind) || !SEVERITIES.has(value?.severity)) return null
-    return {kind: value.kind, ruleId, severity: value.severity, from, to}
-}
-
-export function sanitizeArchitecture(value) {
-    const modules = list(value?.modules, CAPS.modules, moduleFact, (a, b) => compare(a.id, b.id))
-    const dependencies = {}
-    let truncated = modules.truncated
-    const dependencyMeta = {}
-    for (const kind of ['runtime', 'typeOnly', 'compileOnly']) {
-        const result = list(value?.dependencies?.[kind], CAPS.dependencies, dependency, (a, b) => compare(a.from, b.from) || compare(a.to, b.to))
-        dependencies[kind] = result.items
-        const completenessKey = `${kind}Dependencies`
-        dependencyMeta[completenessKey] = count(value?.completeness?.[completenessKey], result.total, result.items.length)
-        truncated ||= result.truncated
-    }
-    const cycles = list(value?.cycles, CAPS.findings, cycleFact, (a, b) => compare(a.kind, b.kind) || b.size - a.size || compare(a.id, b.id))
-    const boundaries = list(value?.boundaryViolations, CAPS.findings, boundaryFact, (a, b) => compare(a.ruleId, b.ruleId) || compare(a.from, b.from) || compare(a.to, b.to))
-    truncated ||= cycles.truncated || boundaries.truncated
-    const outState = state(value?.state)
-    return {
-        state: truncated && outState === 'COMPLETE' ? 'PARTIAL' : outState,
-        verdict: verdict(value?.verdict),
-        completeness: {modules: count(value?.completeness?.modules, modules.total, modules.items.length), ...dependencyMeta, cycles: count(value?.completeness?.cycles, cycles.total, cycles.items.length), boundaryViolations: count(value?.completeness?.boundaryViolations, boundaries.total, boundaries.items.length), reasons: reasons(value?.completeness?.reasons)},
-        modules: modules.items, dependencies, cycles: cycles.items, boundaryViolations: boundaries.items,
-        boundaryRulesState: state(value?.boundaryRulesState),
-    }
-}

package/src/mcp/sync/evidence-common.mjs

@@ -1,88 +0,0 @@
-export const SEVERITIES = new Set(['critical', 'high', 'medium', 'low', 'info'])
-export const CONFIDENCE = new Set(['high', 'medium', 'low'])
-export const CATEGORIES = new Set(['unused', 'structure', 'vulnerability', 'malware'])
-const CHECK_KEYS = ['osv', 'malware']
-export const PACKAGE_DEPENDENCY_KINDS = new Set(['runtime', 'dev', 'optional', 'peer', 'optional-peer'])
-export const CAPS = Object.freeze({
-    modules: 500, dependencies: 2000, findings: 500, hotspots: 250, badges: 100,
-    packages: 5000, usage: 1000, files: 20, packageGraphNodes: 5000, packageGraphEdges: 20000,
-    duplicateGroups: 100, duplicateMembers: 12, divergenceCandidates: 100,
-})
-export const DUPLICATE_THRESHOLDS = Object.freeze({
-    clones: Object.freeze({mode: 'renamed', minSimilarityPercent: 80, minTokens: 50}),
-    divergence: Object.freeze({sameName: true, maxSimilarityPercent: 45, minTokens: 50, maxImplementationsPerName: 12}),
-})
-
-const STATES = new Set(['COMPLETE', 'PARTIAL', 'NOT_CHECKED', 'NOT_APPLICABLE', 'ERROR'])
-const VERDICTS = new Set(['PASS', 'FAIL', 'UNKNOWN'])
-const CONTROL = /[\u0000-\u001f\u007f]/
-const ABSOLUTE_PATH_FRAGMENT = /(?:^|[\/\s"'`(=])[a-z]:[\\/]|(?:^|[\s"'`(=])(?:\\\\[^\\/\s]+(?:[\\/]|$)|file:(?:\/\/)?[\\/]|\/(?!\/)[^\s])/i
-const TOKEN = /^[\p{L}\p{N}_.:@+\-#$<>()\[\],]+$/u
-const PACKAGE = /^(?:@[a-z0-9._-]+\/)?[a-z0-9][a-z0-9._-]*$/i
-
-export const int = (value) => Number.isFinite(value) && value >= 0 ? Math.trunc(value) : 0
-export const bool = (value) => value === true
-export const text = (value, max = 256) => typeof value === 'string' && value.length > 0 && value.length <= max && !CONTROL.test(value) ? value : undefined
-export const token = (value, max = 256) => { const valueText = text(value, max); return valueText && TOKEN.test(valueText) ? valueText : undefined }
-export const privacySafeText = (value, max = 256) => { const valueText = text(value, max); return valueText && !ABSOLUTE_PATH_FRAGMENT.test(valueText) ? valueText : undefined }
-export const packageName = (value) => { const valueText = text(value, 256); return valueText && PACKAGE.test(valueText) ? valueText : undefined }
-export const packageVersion = (value) => { const valueText = text(value, 128); return valueText && /^[A-Za-z0-9][A-Za-z0-9._+~-]*$/.test(valueText) ? valueText : undefined }
-export const state = (value) => STATES.has(value) ? value : 'ERROR'
-export const verdict = (value) => VERDICTS.has(value) ? value : 'UNKNOWN'
-export const compare = (a, b) => String(a).localeCompare(String(b), 'en')
-
-export function path(value, max = 4096) {
-    const raw = text(value, max)
-    if (!raw) return undefined
-    const normalized = raw.replace(/\\/g, '/')
-    if (/^(?:[a-z][a-z0-9+.-]*:|\/)/i.test(normalized)) return undefined
-    const parts = normalized.split('/')
-    return parts.length && parts.every((part) => part && part !== '.' && part !== '..') ? normalized : undefined
-}
-
-export function graphId(value) {
-    const id = text(value, 4096)
-    if (!id) return undefined
-    const hash = id.indexOf('#')
-    const file = hash < 0 ? id : id.slice(0, hash)
-    const safeFile = path(file)
-    if (!safeFile) return undefined
-    if (hash < 0) return safeFile
-    const suffix = id.slice(hash)
-    return suffix.length <= 512 && /^#[^\\/\s\u0000-\u001f\u007f]{1,511}$/u.test(suffix) ? `${safeFile}${suffix}` : undefined
-}
-
-export function moduleId(value) { return value === '(root)' ? value : path(value) }
-export function set(out, key, value) { if (value !== undefined) out[key] = value }
-
-export function stableStringify(value) {
-    if (Array.isArray(value)) return `[${value.map(stableStringify).join(',')}]`
-    if (value && typeof value === 'object') return `{${Object.keys(value).sort(compare).map((key) => `${JSON.stringify(key)}:${stableStringify(value[key])}`).join(',')}}`
-    return JSON.stringify(value)
-}
-
-export function list(values, cap, mapper, sorter) {
-    const all = (Array.isArray(values) ? values : []).map(mapper).filter(Boolean).sort(sorter)
-    return {items: all.slice(0, cap), total: all.length, truncated: all.length > cap}
-}
-
-export function count(value, fallbackTotal, returned) {
-    const total = Math.max(int(value?.total), fallbackTotal)
-    return {total, returned, truncated: bool(value?.truncated) || total > returned}
-}
-
-export function reasons(values) {
-    return [...new Set((Array.isArray(values) ? values : []).map((value) => token(value, 96)).filter(Boolean))].sort(compare).slice(0, 32)
-}
-
-export function numericRecord(value, keys) {
-    const out = {}
-    for (const key of keys) out[key] = int(value?.[key])
-    return out
-}
-
-export function checks(value) {
-    const out = {}
-    for (const key of CHECK_KEYS) out[key] = state(value?.[key])
-    return out
-}