/**
 * Nexus analyze orchestrator — business logic extracted from `cleo nexus analyze`.
 *
 * Stages a replacement code graph and publishes it atomically,
 * refreshes the nexus-bridge, updates the multi-project registry, and sweeps
 * the git log for task–symbol links. Post-publication hooks are best-effort.
 *
 * @module nexus/analyze-orchestrator
 * @epic T9833
 * @task T10062
 */
import type { GraphIndexAssessment, GraphIndexRunSummary, GraphParseCacheEntry, GraphPublicationRows, ParserExecutionLimits } from '@cleocode/contracts';
import type { NodeSQLiteDatabase } from 'drizzle-orm/node-sqlite';
/** Read the parse cache committed with the current generation (T12315). */
export declare function readNexusParseCache(db: NodeSQLiteDatabase): GraphParseCacheEntry[];
/**
 * Persist a batch of parsed extractions outside the graph publication
 * (T14009), so an aborted or killed analysis keeps its parse work. Entries are
 * exact by path, content hash and extractor fingerprint; the next run reuses
 * them, and the publication keeps only its own generation's files.
 *
 * @param db - Project graph database.
 * @param entries - Extractions parsed since the last checkpoint.
 */
export declare function checkpointNexusParseCache(db: NodeSQLiteDatabase, entries: readonly GraphParseCacheEntry[]): void;
/** Receipt of a graph re-bound from a moved project's recorded root to its live root (T12659). */
export interface NexusGraphRebind {
    /** Project root the previous graph was recorded under. */
    oldRoot: string;
    /** Live project root the rebuilt graph is bound to. */
    newRoot: string;
    /** Project id, identical before and after. */
    projectId: string;
    /** Graph generation published by the re-binding rebuild. */
    generation: string | null;
    /** Included repositories dropped because they were missing (only with `dropMissingRepositories`). */
    droppedRepositories: string[];
}
/** Included repositories an analysis dropped because they were missing on disk (T12659). */
export interface NexusDroppedRepositories {
    /** Relative paths dropped from the index scope. */
    paths: string[];
    /** Command that re-includes every dropped path once it exists again. */
    restoreCommand: string;
}
/**
 * Atomically publish staged rows if the graph has not changed since assessment.
 * Failed inserts, FTS repair, or stale generations roll back the entire replacement.
 * Code placed in `packages/core/` per Package-Boundary Check — verified against AGENTS.md.
 * @param db - Owning project graph database with the canonical schema installed.
 * @param rows - Validated staged nodes, relations and source assessment to publish.
 * @param expectedGeneration - Previously observed generation; null for the first publication.
 * @returns The number of node and relation rows written.
 * @remarks The transaction rejects stale generation preconditions and restores the
 * prior live rows on failure. Successful replacement does not itself retain an
 * independently recoverable historical generation.
 * @example
 * ```ts
 * publishNexusGraph(db, stagedRows, expectedGeneration);
 * ```
 */
export declare function publishNexusGraph(db: NodeSQLiteDatabase, rows: GraphPublicationRows, expectedGeneration: string | null): {
    nodeCount: number;
    relationCount: number;
};
/** Parameters for {@link runNexusAnalysis}. */
export interface NexusAnalysisParams {
    /** Per-file parser bounds and cancellation; native RSS containment is unverified. */
    parserLimits?: ParserExecutionLimits;
    /**
     * Epoch milliseconds at which the run's budget ends (T14016): uninterruptible
     * phases start only when their estimate fits what is left.
     */
    deadlineAt?: number;
    /** Absolute path to the repository to analyze. */
    repoPath: string;
    /** Stable identity parent; defaults to repoPath and can differ from the analyzed source. */
    projectRoot?: string;
    /** Explicit existing identity override; otherwise require persisted parent identity. */
    projectIdOverride?: string;
    /**
     * Parse every file instead of reusing the previous generation's extractions.
     * When omitted, an analysis reuses what is provably current (T12315) and
     * falls back to a full parse — reporting why — when it cannot.
     */
    full?: boolean;
    /**
     * @deprecated Incremental reuse is the default since T12315; this flag is
     * accepted for compatibility and has no effect. Use `full` to force a rebuild.
     */
    incremental?: boolean;
    /** Explicit relative paths of nested repositories authorized for source inclusion. */
    includedRepositories?: readonly string[];
    /** Refuse a run that would be a full rebuild (T13523: inline refresh from a read query). */
    requireIncremental?: boolean;
    /**
     * Drop included repositories (explicit or carried over) that are missing on
     * disk instead of refusing. Off by default: a missing inclusion refuses and
     * keeps the previous graph (T12659). Dropped paths are reported with a
     * restore command in {@link NexusAnalysisResult.droppedRepositories}.
     */
    dropMissingRepositories?: boolean;
    /**
     * Progress callback invoked every 50 files (and on completion).
     * Omit for JSON output mode.
     */
    onProgress?: (current: number, total: number, filePath: string) => void;
}
/** Result of a successful {@link runNexusAnalysis} call. */
export interface NexusAnalysisResult {
    projectId: string;
    repoPath: string;
    /** Whether this run reused previous extractions (mode `incremental` or `unchanged`). */
    incremental: boolean;
    /** Mode, reason, per-file counts and phase costs of this run. */
    summary: GraphIndexRunSummary;
    nodeCount: number;
    relationCount: number;
    fileCount: number;
    durationMs: number;
    /**
     * Committed per-file outcomes and source provenance, as a summary: the
     * reference list is reported as `referenceCount` (T12348).
     */
    assessment: GraphIndexAssessment | null;
    /**
     * Present when a `--full` run re-bound a moved project's graph (same project
     * id, different recorded root) to the live root (T12659).
     */
    rebind?: NexusGraphRebind;
    /**
     * Included repositories dropped because they were missing on disk, only with
     * `dropMissingRepositories` (T12659), and the one command that restores them
     * once they are back.
     */
    droppedRepositories?: NexusDroppedRepositories;
}
/**
 * Run the nexus code-intelligence pipeline on a repository.
 *
 * This function:
 * 1. Captures the existing parent identity and explicit source roots.
 * 2. Captures the current graph generation for concurrent-write detection.
 * 3. Stages and atomically publishes the `@cleocode/nexus` pipeline output.
 * 4. Best-effort: refreshes `nexus-bridge.md`.
 * 5. Best-effort: updates the multi-project registry.
 * 6. Best-effort: sweeps the git log for task–symbol links.
 *
 * @param params - Analysis configuration
 * @returns Pipeline result with node/relation/file counts and duration
 * @throws {Error} When identity, source preconditions or the pipeline fail.
 * @remarks Root revisions and file hashes are optimistic preconditions, not a
 * filesystem lock. Publication uses the owning store's synchronous generation CAS;
 * optional post-publication hooks cannot replace its committed result.
 * @example
 * ```ts
 * const result = await runNexusAnalysis({ repoPath: '/identity', includedRepositories: ['app'] });
 * ```
 */
export declare function runNexusAnalysis(params: NexusAnalysisParams): Promise<NexusAnalysisResult>;
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