@specship/specship-darwin-arm64 0.29.0 → 0.30.0

package/lib/dist/index.d.ts

@@ -22,6 +22,7 @@ import { EnforceConfig, EnforceReport, EnforceScope } from './enforce/enforce';
 import { BehaviourSurface } from './behaviour/behaviour-surface';
 import { FlowDiagramOptions, FlowDiagramResult } from './diagram/flow-diagram';
 import { WatchOptions, PendingFile } from './sync';
+import { IndexFreshness } from './sync/worktree';
 export * from './types';
 export { getDatabasePath, DatabaseConnection } from './db';
 export { QueryBuilder } from './db/queries';
@@ -44,15 +45,16 @@ export { computeMaintainability, resolveThresholds, resolveExclude, DEFAULT_THRE
 export { collectFlows, renderMermaidFlowchart, writeFlowDiagramIfChanged, shouldAutoRefreshDiagram, resolveDiagramConfig, DEFAULT_DIAGRAM_OPTIONS } from './diagram/flow-diagram';
 export type { FlowDiagramOptions, FlowDiagramConfig, FlowDiagramResult, FlowGraph } from './diagram/flow-diagram';
 export { evaluateFitness, loadFitnessRules, FITNESS_CONFIG_FILE } from './fitness/fitness';
-export { evaluateEnforcement, loadEnforceConfig, ENFORCE_CONFIG_FILE, normalizePath } from './enforce/enforce';
-export { changedFilesSince, InvalidRefError, workingTreeDiffText } from './enforce/changed-files';
+export { evaluateEnforcement, loadEnforceConfig, ENFORCE_CONFIG_FILE, normalizePath, undeclaredLinkFindings, branchBrokenFindings } from './enforce/enforce';
+export { changedFilesSince, InvalidRefError, workingTreeDiffText, existedAtRef } from './enforce/changed-files';
 export { scanDisableComments, formatSuppressionFinding } from './enforce/suppressions';
 export type { SuppressionFinding } from './enforce/suppressions';
+export type { IndexFreshness, IndexStaleReason } from './sync/worktree';
 export { parseMutationReport, loadMutationDeps, DEFAULT_MUTATION_THRESHOLD, DEFAULT_MUTATION_REPORT } from './enforce/mutation';
 export type { MutationConfig, MutationDeps, MutationFileStats } from './enforce/mutation';
 export { computeBehaviourSurface, renderBehaviourSurface, isUiNode, classifyCriterionShape, propertyFramework } from './behaviour/behaviour-surface';
 export type { BehaviourSurface, BehaviourFlowElement, BehaviourSurfaceDeps } from './behaviour/behaviour-surface';
-export type { EnforceConfig, GateConfig, EnforceReport, EnforceDeps, EnforceScope, CheckOutcome, CheckName, RequirementVerification, } from './enforce/enforce';
+export type { EnforceConfig, GateConfig, EnforceReport, EnforceDeps, EnforceScope, CheckOutcome, CheckName, RequirementVerification, BrokenAtRefEntry, } from './enforce/enforce';
 export type { FitnessRule, ForbiddenRule, LayersRule, IsolationRule, FitnessReport, FitnessViolation, FitnessConfigError, Selector, } from './fitness/fitness';
 export type { MaintainabilityReport, MaintainabilityThresholds, CouplingFinding, OversizedFinding, GodFileFinding, CycleFinding, DeadCodeFinding, } from './graph/maintainability';
 export { SpecShipError, FileError, ParseError, DatabaseError, SearchError, VectorError, ConfigError, Logger, setLogger, getLogger, silentLogger, defaultLogger, } from './errors';
@@ -185,6 +187,22 @@ export declare class SpecShip {
      * gate evaluates the whole repository exactly as before.
      */
     getEnforce(config?: EnforceConfig, scope?: EnforceScope): EnforceReport;
+    /**
+     * Load the grammars `getEnforce` needs to parse link-target files at a
+     * `--since` ref (REQ-MULTIDEV-002). `getEnforce` is synchronous; call this
+     * first. Without it a target whose grammar isn't loaded counts as not
+     * resolving at the ref, so it is never reported (silent beats wrong).
+     */
+    prepareEnforce(scope?: EnforceScope): Promise<void>;
+    /**
+     * Each orphaned/broken link, marked with whether its target resolved at
+     * `ref` (REQ-MULTIDEV-002.A2/A3). Reads the file's blob from git and parses
+     * it in memory — no index of the ref is needed. The qualified-name match is
+     * the spec-link resolver's (every `.` ⇄ `::` separator variant), so a
+     * spec-declared `Class.method` finds an extracted `Class::method`. Each
+     * file is parsed once.
+     */
+    private linksBrokenSinceRef;
     /**
      * The behaviour surface for a requirement (REQ-BEHAVIOUR-001): its linked code
      * plus the 1-hop route / component / handler neighbourhood, grouped UI vs
@@ -292,6 +310,20 @@ export declare class SpecShip {
      * Uses a mutex to prevent concurrent indexing operations.
      */
     indexAll(options?: IndexOptions): Promise<IndexResult>;
+    /**
+     * Record the git branch, commit and uncommitted-tracked-state fingerprint
+     * this index was built against (REQ-MULTIDEV-004). Called only at the end of
+     * a full `indexAll()` / `sync()` — never from `indexFiles()` — so the record
+     * always describes a complete pass. Outside git it writes nothing.
+     * Best-effort: never fails the index.
+     */
+    private recordIndexedRevision;
+    /**
+     * Compare the recorded index revision with the checkout's live HEAD and
+     * uncommitted tracked state (REQ-MULTIDEV-004). Read-only: never syncs.
+     * Null outside git or when no revision was recorded.
+     */
+    getIndexFreshness(): IndexFreshness | null;
     /**
      * Refresh `.specship/statusline.json` so the `specship statusline` segment
      * has current Tier-A data without ever opening the DB itself
@@ -327,6 +359,18 @@ export declare class SpecShip {
      * drift rule over the surviving rows.
      */
     private replaceSpecsForFile;
+    /**
+     * Remove `code-comment` links the last full pass did not re-derive
+     * (REQ-MULTIDEV-006): the `@implements` / `@verifies` marker, the test
+     * title naming the requirement, or the whole file is gone. A link the spec
+     * file still declares is kept and re-labelled as a declaration, with its
+     * state and evidence untouched (A4). Links in files that could not be read
+     * are left alone. Removed links are not drift, so nothing is reported.
+     *
+     * Must run only after BOTH code-derived passes over every indexed file —
+     * a partial pass would take the links of the files it skipped.
+     */
+    private reconcileCodeDerivedLinks;
     /**
      * Internal spec indexing — does NOT take the indexMutex (caller already holds it)
      * and does NOT take the fileLock. Used by indexAll and sync, which manage locks
@@ -363,12 +407,28 @@ export declare class SpecShip {
     indexSpecs(roots?: string[]): Promise<{
         filesProcessed: number;
         filesSkipped: number;
+        /** Spec files pruned because they no longer exist (REQ-MULTIDEV-003). */
+        filesRemoved: number;
         specsExtracted: number;
         linkCandidates: number;
         resolverStats: SpecLinkResolverStats;
         errors: number;
         durationMs: number;
     }>;
+    /**
+     * Remove indexed spec files that no longer exist in the checkout — a
+     * deleted file, or one missing on the branch just checked out
+     * (REQ-MULTIDEV-003). `deleteSpecFile` cascades to the file's specs,
+     * acceptance criteria, links and virtual `spec` nodes, so the removed links
+     * never reach drift. No drift transitions are emitted.
+     *
+     * A row is pruned only when its path was not collected this pass AND is
+     * absent on disk — a file that merely failed to read keeps its rows. With
+     * explicit `roots`, only rows under those roots are considered.
+     *
+     * Returns the number of spec files removed.
+     */
+    private pruneMissingSpecFiles;
     /**
      * Default spec roots: `<projectRoot>/specs/` if it exists. Future
      * iterations can read from `.specship/config.json`.

package/lib/dist/index.d.ts.map

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package/lib/dist/index.js

@@ -43,7 +43,7 @@ var __exportStar = (this && this.__exportStar) || function(m, exports) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.writeFlowDiagramIfChanged = exports.renderMermaidFlowchart = exports.collectFlows = exports.highPrecisionClean = exports.LOW_CONFIDENCE_CLASSES = exports.HIGH_PRECISION_CLASSES = exports.CONFIG_FILE_NAME = exports.DEFAULT_EXCLUDE = exports.DEFAULT_THRESHOLDS = exports.resolveExclude = exports.resolveThresholds = exports.computeMaintainability = exports.undoProposal = exports.applyProposal = exports.previewProposal = exports.ReflectStore = exports.reflectSweep = exports.reflectAnalyze = exports.scanTestTitleRefs = exports.isNonTestEvidence = exports.isRecognizedTestFile = exports.TestReportParseError = exports.caseMatchesLink = exports.parseVitestJsonReport = exports.ingestTestReport = exports.requireKindsExitCode = exports.criteriaMissingKind = exports.evidenceKindCoverage = exports.verdictFor = exports.formatCoverageLine = exports.computeSpecCoverage = exports.computeDomainGapSeed = exports.findBriefsForSpec = exports.summarizeBriefFunnel = exports.resolveBriefLink = exports.computeSpecFunnel = exports.loadAllGrammars = exports.loadGrammarsForLanguages = exports.initGrammars = exports.getSupportedLanguages = exports.isGrammarLoaded = exports.isLanguageSupported = exports.detectLanguage = exports.SPECSHIP_DIR = exports.findNearestSpecShipRoot = exports.isInitialized = exports.getSpecShipDir = exports.QueryBuilder = exports.DatabaseConnection = exports.getDatabasePath = void 0;
-exports.SpecShip = exports.MCPServer = exports.LockUnavailableError = exports.FileWatcher = exports.MemoryMonitor = exports.throttle = exports.debounce = exports.processInBatches = exports.FileLock = exports.Mutex = exports.defaultLogger = exports.silentLogger = exports.getLogger = exports.setLogger = exports.ConfigError = exports.VectorError = exports.SearchError = exports.DatabaseError = exports.ParseError = exports.FileError = exports.SpecShipError = exports.propertyFramework = exports.classifyCriterionShape = exports.isUiNode = exports.renderBehaviourSurface = exports.computeBehaviourSurface = exports.DEFAULT_MUTATION_REPORT = exports.DEFAULT_MUTATION_THRESHOLD = exports.loadMutationDeps = exports.parseMutationReport = exports.formatSuppressionFinding = exports.scanDisableComments = exports.workingTreeDiffText = exports.InvalidRefError = exports.changedFilesSince = exports.normalizePath = exports.ENFORCE_CONFIG_FILE = exports.loadEnforceConfig = exports.evaluateEnforcement = exports.FITNESS_CONFIG_FILE = exports.loadFitnessRules = exports.evaluateFitness = exports.DEFAULT_DIAGRAM_OPTIONS = exports.resolveDiagramConfig = exports.shouldAutoRefreshDiagram = void 0;
+exports.SpecShip = exports.MCPServer = exports.LockUnavailableError = exports.FileWatcher = exports.MemoryMonitor = exports.throttle = exports.debounce = exports.processInBatches = exports.FileLock = exports.Mutex = exports.defaultLogger = exports.silentLogger = exports.getLogger = exports.setLogger = exports.ConfigError = exports.VectorError = exports.SearchError = exports.DatabaseError = exports.ParseError = exports.FileError = exports.SpecShipError = exports.propertyFramework = exports.classifyCriterionShape = exports.isUiNode = exports.renderBehaviourSurface = exports.computeBehaviourSurface = exports.DEFAULT_MUTATION_REPORT = exports.DEFAULT_MUTATION_THRESHOLD = exports.loadMutationDeps = exports.parseMutationReport = exports.formatSuppressionFinding = exports.scanDisableComments = exports.existedAtRef = exports.workingTreeDiffText = exports.InvalidRefError = exports.changedFilesSince = exports.branchBrokenFindings = exports.undeclaredLinkFindings = exports.normalizePath = exports.ENFORCE_CONFIG_FILE = exports.loadEnforceConfig = exports.evaluateEnforcement = exports.FITNESS_CONFIG_FILE = exports.loadFitnessRules = exports.evaluateFitness = exports.DEFAULT_DIAGRAM_OPTIONS = exports.resolveDiagramConfig = exports.shouldAutoRefreshDiagram = void 0;
 const path = __importStar(require("path"));
 const db_1 = require("./db");
 const queries_1 = require("./db/queries");
@@ -73,8 +73,11 @@ const changed_files_1 = require("./enforce/changed-files");
 const behaviour_surface_1 = require("./behaviour/behaviour-surface");
 const flow_diagram_1 = require("./diagram/flow-diagram");
 const context_1 = require("./context");
+const hook_output_1 = require("./activation/hook-output");
+const detect_1 = require("./agents/detect");
 const utils_1 = require("./utils");
 const sync_1 = require("./sync");
+const worktree_1 = require("./sync/worktree");
 // Re-export types for consumers
 __exportStar(require("./types"), exports);
 // Storage building blocks for embedded/SDK consumers that drive the graph
@@ -160,11 +163,14 @@ Object.defineProperty(exports, "evaluateEnforcement", { enumerable: true, get: f
 Object.defineProperty(exports, "loadEnforceConfig", { enumerable: true, get: function () { return enforce_2.loadEnforceConfig; } });
 Object.defineProperty(exports, "ENFORCE_CONFIG_FILE", { enumerable: true, get: function () { return enforce_2.ENFORCE_CONFIG_FILE; } });
 Object.defineProperty(exports, "normalizePath", { enumerable: true, get: function () { return enforce_2.normalizePath; } });
+Object.defineProperty(exports, "undeclaredLinkFindings", { enumerable: true, get: function () { return enforce_2.undeclaredLinkFindings; } });
+Object.defineProperty(exports, "branchBrokenFindings", { enumerable: true, get: function () { return enforce_2.branchBrokenFindings; } });
 // Change-scoped gating (REQ-AUTHG-006) — `specship check --since <ref>`.
 var changed_files_2 = require("./enforce/changed-files");
 Object.defineProperty(exports, "changedFilesSince", { enumerable: true, get: function () { return changed_files_2.changedFilesSince; } });
 Object.defineProperty(exports, "InvalidRefError", { enumerable: true, get: function () { return changed_files_2.InvalidRefError; } });
 Object.defineProperty(exports, "workingTreeDiffText", { enumerable: true, get: function () { return changed_files_2.workingTreeDiffText; } });
+Object.defineProperty(exports, "existedAtRef", { enumerable: true, get: function () { return changed_files_2.existedAtRef; } });
 // Suppression-comment scan (REQ-QGATE-004).
 var suppressions_2 = require("./enforce/suppressions");
 Object.defineProperty(exports, "scanDisableComments", { enumerable: true, get: function () { return suppressions_2.scanDisableComments; } });
@@ -370,7 +376,67 @@ class SpecShip {
         const mutation = cfg.mutation !== undefined || cfg.gate?.mutation === true
             ? (0, mutation_1.loadMutationDeps)(this.projectRoot, cfg.mutation)
             : undefined;
-        return (0, enforce_1.evaluateEnforcement)({ drift, fitness: this.getFitness(), maintainability: this.getMaintainability(), requirements, suppressions, mutation }, cfg, scope);
+        // Merge checks (REQ-MULTIDEV-002): every link row feeds the
+        // undeclared-links check; a `--since` run also compares each currently
+        // orphaned/broken link against its file's blob at the ref.
+        const links = sq.getAllLinks();
+        const brokenAtRef = scope?.since ? this.linksBrokenSinceRef(scope.since) : undefined;
+        return (0, enforce_1.evaluateEnforcement)({
+            drift, fitness: this.getFitness(), maintainability: this.getMaintainability(), requirements, suppressions, mutation,
+            links, brokenAtRef,
+        }, cfg, scope);
+    }
+    /**
+     * Load the grammars `getEnforce` needs to parse link-target files at a
+     * `--since` ref (REQ-MULTIDEV-002). `getEnforce` is synchronous; call this
+     * first. Without it a target whose grammar isn't loaded counts as not
+     * resolving at the ref, so it is never reported (silent beats wrong).
+     */
+    async prepareEnforce(scope) {
+        if (!scope?.since)
+            return;
+        const files = new Set(this.specQueries.getLinksByState(['orphaned', 'broken']).map((l) => l.targetFilePath));
+        if (files.size === 0)
+            return;
+        await (0, extraction_1.initGrammars)();
+        await (0, extraction_1.loadGrammarsForLanguages)([...files].map((f) => (0, extraction_1.detectLanguage)(f)));
+    }
+    /**
+     * Each orphaned/broken link, marked with whether its target resolved at
+     * `ref` (REQ-MULTIDEV-002.A2/A3). Reads the file's blob from git and parses
+     * it in memory — no index of the ref is needed. The qualified-name match is
+     * the spec-link resolver's (every `.` ⇄ `::` separator variant), so a
+     * spec-declared `Class.method` finds an extracted `Class::method`. Each
+     * file is parsed once.
+     */
+    linksBrokenSinceRef(ref) {
+        const namesAtRef = new Map();
+        const namesIn = (file) => {
+            const cached = namesAtRef.get(file);
+            if (cached)
+                return cached;
+            const names = new Set();
+            const blob = (0, changed_files_1.existedAtRef)(this.projectRoot, ref, file);
+            if (blob !== null) {
+                try {
+                    for (const n of (0, extraction_1.extractFromSource)(file, blob).nodes) {
+                        // Exact qualified name only — the resolver's getNodesByQualifiedNameExact.
+                        if (n.qualifiedName)
+                            names.add(n.qualifiedName);
+                    }
+                }
+                catch {
+                    // unparseable at the ref → treated as unresolved
+                }
+            }
+            namesAtRef.set(file, names);
+            return names;
+        };
+        return this.specQueries.getLinksByState(['orphaned', 'broken']).map((link) => {
+            const names = namesIn(link.targetFilePath);
+            const resolvedAtRef = (0, spec_link_resolver_1.qualifiedNameVariants)(link.targetQualifiedName).some((v) => names.has(v));
+            return { link, resolvedAtRef, ref };
+        });
     }
     /**
      * The behaviour surface for a requirement (REQ-BEHAVIOUR-001): its linked code
@@ -469,7 +535,14 @@ class SpecShip {
         catch {
             domainGapEntities = undefined;
         }
-        return { projectRoot: this.projectRoot, homeDir: os.homedir(), domainGapEntities };
+        // Proposals target the agent this process serves (REQ-AGENTSWITCH-003);
+        // an undetectable agent maps to the default host.
+        return {
+            projectRoot: this.projectRoot,
+            homeDir: os.homedir(),
+            domainGapEntities,
+            host: (0, hook_output_1.hostTraitsFor)((0, detect_1.agentFromEnv)()),
+        };
     }
     /**
      * Estimated time-to-completion for a workflow run (WORKFLOW-ETA-DOC):
@@ -767,6 +840,8 @@ class SpecShip {
                 catch {
                     /* a diagram fault must never fail an index */
                 }
+                if (result.success)
+                    this.recordIndexedRevision();
                 this.refreshStatuslineCache();
                 return result;
             }
@@ -775,6 +850,50 @@ class SpecShip {
             }
         });
     }
+    /**
+     * Record the git branch, commit and uncommitted-tracked-state fingerprint
+     * this index was built against (REQ-MULTIDEV-004). Called only at the end of
+     * a full `indexAll()` / `sync()` — never from `indexFiles()` — so the record
+     * always describes a complete pass. Outside git it writes nothing.
+     * Best-effort: never fails the index.
+     */
+    recordIndexedRevision() {
+        try {
+            const head = (0, worktree_1.readGitHead)(this.projectRoot);
+            if (!head)
+                return;
+            this.queries.setMetadata('indexed_commit', head.commit);
+            this.queries.setMetadata('indexed_branch', head.branch ?? '');
+            this.queries.setMetadata('indexed_worktree_fingerprint', (0, worktree_1.uncommittedTrackedFingerprint)(this.projectRoot) ?? '');
+        }
+        catch {
+            /* best-effort */
+        }
+    }
+    /**
+     * Compare the recorded index revision with the checkout's live HEAD and
+     * uncommitted tracked state (REQ-MULTIDEV-004). Read-only: never syncs.
+     * Null outside git or when no revision was recorded.
+     */
+    getIndexFreshness() {
+        try {
+            const indexedCommit = this.queries.getMetadata('indexed_commit');
+            if (!indexedCommit)
+                return null;
+            const head = (0, worktree_1.readGitHead)(this.projectRoot);
+            if (!head)
+                return null;
+            const indexedBranch = this.queries.getMetadata('indexed_branch') || null;
+            const recordedFp = this.queries.getMetadata('indexed_worktree_fingerprint');
+            const currentFp = (0, worktree_1.uncommittedTrackedFingerprint)(this.projectRoot);
+            // Unknown on either side → don't claim a working-tree change (silent beats wrong).
+            const worktreeChanged = !!recordedFp && !!currentFp && recordedFp !== currentFp;
+            return (0, worktree_1.computeIndexFreshness)({ branch: indexedBranch, commit: indexedCommit }, head, worktreeChanged);
+        }
+        catch {
+            return null;
+        }
+    }
     /**
      * Refresh `.specship/statusline.json` so the `specship statusline` segment
      * has current Tier-A data without ever opening the DB itself
@@ -850,6 +969,57 @@ class SpecShip {
         }
         return result;
     }
+    /**
+     * Remove `code-comment` links the last full pass did not re-derive
+     * (REQ-MULTIDEV-006): the `@implements` / `@verifies` marker, the test
+     * title naming the requirement, or the whole file is gone. A link the spec
+     * file still declares is kept and re-labelled as a declaration, with its
+     * state and evidence untouched (A4). Links in files that could not be read
+     * are left alone. Removed links are not drift, so nothing is reported.
+     *
+     * Must run only after BOTH code-derived passes over every indexed file —
+     * a partial pass would take the links of the files it skipped.
+     */
+    // @implements REQ-MULTIDEV-006
+    reconcileCodeDerivedLinks(derived) {
+        const declaredBySource = new Map();
+        const declaredKeys = (sourcePath) => {
+            let keys = declaredBySource.get(sourcePath);
+            if (keys)
+                return keys;
+            keys = new Set();
+            try {
+                const abs = path.isAbsolute(sourcePath) ? sourcePath : path.join(this.projectRoot, sourcePath);
+                const result = new markdown_spec_extractor_1.MarkdownSpecExtractor(sourcePath, fs.readFileSync(abs, 'utf-8')).extract();
+                for (const c of result.linkCandidates) {
+                    keys.add((0, spec_link_resolver_1.codeDerivedLinkKey)(c.specId, c.targetFilePath, (0, spec_link_resolver_1.canonicalQualifiedName)(c.targetQualifiedName), c.kind));
+                }
+            }
+            catch {
+                // An unreadable spec declares nothing we can see; its spec rows are
+                // pruned separately (REQ-MULTIDEV-003).
+            }
+            declaredBySource.set(sourcePath, keys);
+            return keys;
+        };
+        let removed = 0;
+        const now = Date.now();
+        for (const link of this.specQueries.getLinksByProvenance('code-comment')) {
+            if (derived.unreadFiles.has(link.targetFilePath))
+                continue;
+            const key = (0, spec_link_resolver_1.codeDerivedLinkKey)(link.specId, link.targetFilePath, link.targetQualifiedName, link.kind);
+            if (derived.keys.has(key))
+                continue;
+            const spec = this.specQueries.getSpecById(link.specId);
+            if (spec && declaredKeys(spec.sourcePath).has(key)) {
+                this.specQueries.setSpecLinkProvenance(link.id, 'spec-declaration', 0.7, now);
+                continue;
+            }
+            this.specQueries.deleteSpecLink(link.id);
+            removed++;
+        }
+        return removed;
+    }
     /**
      * Internal spec indexing — does NOT take the indexMutex (caller already holds it)
      * and does NOT take the fileLock. Used by indexAll and sync, which manage locks
@@ -873,13 +1043,15 @@ class SpecShip {
             candidatesApplied: 0, commentLinksApplied: 0, reattached: 0, transitions,
         };
         let specFilesChanged = 0;
+        // No early return when specs/ is missing: a checkout without the
+        // directory must still prune the rows of files that are gone
+        // (REQ-MULTIDEV-003).
         const specRoots = this.defaultSpecRoots();
-        if (specRoots.length === 0)
-            return { transitions, errors: totalErrors, warnings: totalWarnings };
         const specFiles = [];
         for (const root of specRoots) {
             this.collectSpecFiles(root, specFiles);
         }
+        const present = new Set(specFiles.map((p) => path.relative(this.projectRoot, p)));
         for (const absPath of specFiles) {
             const rel = path.relative(this.projectRoot, absPath);
             let source;
@@ -915,10 +1087,17 @@ class SpecShip {
                 this.specLinkResolver.markSpecDrifted(spec.id, spec.contentHash, specStats);
             }
         }
+        // Prune AFTER the per-file loop: a spec id that moved from a.md to b.md
+        // has already been re-homed (source_path = b.md), so deleting a.md's rows
+        // by source_path cannot take it (REQ-MULTIDEV-003, REQ-VSTATE-001).
+        specFilesChanged += this.pruneMissingSpecFiles(present);
         if (specFilesChanged > 0 || forceResolve) {
             const allFiles = this.queries.getAllFiles().map((f) => f.path);
-            this.specLinkResolver.applyCodeCommentLinks(allFiles);
-            this.specLinkResolver.applyTestTitleLinks(allFiles, specStats);
+            const derived = { keys: new Set(), unreadFiles: new Set() };
+            this.specLinkResolver.applyCodeCommentLinks(allFiles, undefined, derived);
+            this.specLinkResolver.applyTestTitleLinks(allFiles, specStats, derived);
+            // Drop code-derived links whose marker or file is gone (REQ-MULTIDEV-006).
+            this.reconcileCodeDerivedLinks(derived);
             const resolveStats = this.specLinkResolver.resolveAll();
             transitions.push(...resolveStats.transitions);
         }
@@ -952,6 +1131,7 @@ class SpecShip {
                 return {
                     filesProcessed: 0,
                     filesSkipped: 0,
+                    filesRemoved: 0,
                     specsExtracted: 0,
                     linkCandidates: 0,
                     resolverStats: {
@@ -1033,15 +1213,22 @@ class SpecShip {
                     totalCandidates += result.linkCandidates.length;
                     totalErrors += result.errors.filter((e) => e.severity === 'error').length;
                 }
+                // Drop specs whose spec file is gone (REQ-MULTIDEV-003). Explicit
+                // roots scope the prune to those roots; default roots prune all.
+                const present = new Set(specFiles.map((p) => path.relative(this.projectRoot, p)));
+                const filesRemoved = this.pruneMissingSpecFiles(present, roots && roots.length > 0 ? roots : undefined);
                 // After spec changes settle, also scan code docstrings for
                 // `@implements REQ-X` markers. Bounded to the files that already
                 // have nodes in the graph (full-graph scan is acceptable here —
                 // node count is bounded and the scan is O(N) regex over docstrings).
                 const allFiles = this.queries.getAllFiles().map((f) => f.path);
-                this.specLinkResolver.applyCodeCommentLinks(allFiles, stats);
+                const derived = { keys: new Set(), unreadFiles: new Set() };
+                this.specLinkResolver.applyCodeCommentLinks(allFiles, stats, derived);
                 // Spec ids inside `it()` titles in test files → `tests` links
                 // (REQ-VSTATE-002).
-                this.specLinkResolver.applyTestTitleLinks(allFiles, stats);
+                this.specLinkResolver.applyTestTitleLinks(allFiles, stats, derived);
+                // Drop code-derived links whose marker or file is gone (REQ-MULTIDEV-006).
+                this.reconcileCodeDerivedLinks(derived);
                 // Re-resolve all links (post-extraction).
                 const resolveStats = this.specLinkResolver.resolveAll();
                 stats.scanned += resolveStats.scanned;
@@ -1053,6 +1240,7 @@ class SpecShip {
                 return {
                     filesProcessed: processed,
                     filesSkipped: skipped,
+                    filesRemoved,
                     specsExtracted: totalSpecs,
                     linkCandidates: totalCandidates,
                     resolverStats: stats,
@@ -1065,6 +1253,43 @@ class SpecShip {
             }
         });
     }
+    /**
+     * Remove indexed spec files that no longer exist in the checkout — a
+     * deleted file, or one missing on the branch just checked out
+     * (REQ-MULTIDEV-003). `deleteSpecFile` cascades to the file's specs,
+     * acceptance criteria, links and virtual `spec` nodes, so the removed links
+     * never reach drift. No drift transitions are emitted.
+     *
+     * A row is pruned only when its path was not collected this pass AND is
+     * absent on disk — a file that merely failed to read keeps its rows. With
+     * explicit `roots`, only rows under those roots are considered.
+     *
+     * Returns the number of spec files removed.
+     */
+    pruneMissingSpecFiles(present, roots) {
+        const scopes = roots?.map((r) => {
+            const rel = path.relative(this.projectRoot, path.resolve(this.projectRoot, r));
+            return rel === '' ? '' : rel.split(path.sep).join('/');
+        });
+        const inScope = (p) => {
+            if (!scopes)
+                return true;
+            const norm = p.split(path.sep).join('/');
+            return scopes.some((s) => s === '' || norm === s || norm.startsWith(s + '/'));
+        };
+        let removed = 0;
+        for (const row of this.specQueries.getAllSpecFiles()) {
+            if (present.has(row.path))
+                continue;
+            if (!inScope(row.path))
+                continue;
+            if (fs.existsSync(path.join(this.projectRoot, row.path)))
+                continue;
+            this.specQueries.deleteSpecFile(row.path);
+            removed++;
+        }
+        return removed;
+    }
     /**
      * Default spec roots: `<projectRoot>/specs/` if it exists. Future
      * iterations can read from `.specship/config.json`.
@@ -1251,6 +1476,7 @@ class SpecShip {
                 catch {
                     /* a diagram fault must never fail a sync */
                 }
+                this.recordIndexedRevision();
                 this.refreshStatuslineCache();
                 return result;
             }