@phren/cli/dist/tools/finding.js

Knowledge layer for AI agents - CLI, MCP server, and data layer

import { nonInteractiveGitEnv } from "../utils-helpers.js";
import { mcpResponse, resolveStoreForProject } from "./types.js";
import { z } from "zod";
import * as fs from "fs";
import * as path from "path";
import { logger } from "../logger.js";
import { isValidProjectName, errorMessage } from "../utils.js";
import { storeAwareProjectPath } from "../store-routing.js";
import { removeFinding as removeFindingCore, removeFindings as removeFindingsCore, applyFindingTypePrefix, } from "../core/finding.js";
import { debugLog, EXEC_TIMEOUT_MS, FINDING_TYPES, normalizeMemoryScope, } from "../shared.js";
import { getCurrentActor, getMachineName, storeCommitMessage } from "../machine-identity.js";
import { loadCodePackage } from "../modules/code-package.js";
import { moduleEnabled } from "../modules/runtime.js";
import { addFindingToFile, addFindingsToFile, checkSemanticConflicts, } from "../shared/content.js";
import { jaccardTokenize, jaccardSimilarity, stripMetadata, detectConflicts, extractDynamicEntities } from "../content/dedup.js";
import { scanForSecrets } from "../content/secrets.js";
import { runCustomHooks } from "../hooks.js";
import { incrementSessionFindings } from "./session.js";
import { extractFragmentNames } from "../shared/fragment-graph.js";
import { extractFactFromFinding } from "./extract-facts.js";
import { appendChildFinding, editFinding as editFindingCore, readFindings, FINDINGS_FILENAME } from "../data/access.js";
import { getActiveTaskForSession } from "../task/lifecycle.js";
import { isInactiveFindingLine, supersedeFinding, retractFinding as retractFindingLifecycle, resolveFindingContradiction, } from "../finding/lifecycle.js";
import { permissionDeniedError } from "../governance/rbac.js";
import { TEAM_STORE_PATHSPECS } from "../cli/session-git.js";
import { withFileLock } from "../governance/locks.js";
import { runtimeFile } from "../phren-paths.js";
import { mergeStoreUpstream } from "../sync/store-merge.js";
const JACCARD_MAYBE_LOW = 0.25;
const JACCARD_MAYBE_HIGH = 0.40; // above this isDuplicateFinding already catches it
function findJaccardCandidates(phrenPath, project, finding) {
    try {
        const findingsPath = path.join(phrenPath, project, FINDINGS_FILENAME);
        if (!fs.existsSync(findingsPath))
            return [];
        const content = fs.readFileSync(findingsPath, "utf8");
        const newClean = stripMetadata(finding).trim();
        const newTokens = jaccardTokenize(newClean);
        if (newTokens.size < 3)
            return [];
        const candidates = [];
        for (const line of content.split("\n")) {
            if (!line.startsWith("- ") || isInactiveFindingLine(line))
                continue;
            const existingClean = stripMetadata(line).replace(/^-\s+/, "").trim();
            const existingTokens = jaccardTokenize(existingClean);
            if (existingTokens.size < 3)
                continue;
            const sim = jaccardSimilarity(newTokens, existingTokens);
            if (sim >= JACCARD_MAYBE_LOW && sim < JACCARD_MAYBE_HIGH) {
                candidates.push({ existing: existingClean, similarity: Math.round(sim * 100) / 100 });
            }
        }
        return candidates;
    }
    catch {
        return [];
    }
}
// Heuristic conflict candidates surfaced to the calling agent so it can decide whether a
// genuine contradiction exists — no extra LLM/API call, the agent in the loop is the judge.
// Mirrors findJaccardCandidates (potential duplicates). Capped to keep the response small.
const MAX_CONFLICT_CANDIDATES = 5;
export function findConflictCandidates(phrenPath, project, finding) {
    try {
        const findingsPath = path.join(phrenPath, project, FINDINGS_FILENAME);
        if (!fs.existsSync(findingsPath))
            return [];
        const content = fs.readFileSync(findingsPath, "utf8");
        const activeBullets = content.split("\n").filter((l) => l.startsWith("- ") && !isInactiveFindingLine(l));
        if (activeBullets.length === 0)
            return [];
        const dynamicEntities = extractDynamicEntities(phrenPath, project);
        return detectConflicts(finding, activeBullets, dynamicEntities)
            .map((line) => stripMetadata(line).replace(/^-\s+/, "").trim().slice(0, 80))
            .filter((snippet) => snippet.length > 0)
            .slice(0, MAX_CONFLICT_CANDIDATES);
    }
    catch (err) {
        logger.debug("add_finding", `findConflictCandidates: ${errorMessage(err)}`);
        return [];
    }
}
function extractConflictsWith(annotations) {
    return annotations
        .map((annotation) => annotation.match(/<!--\s*conflicts_with:\s*"([^"]+)"/)?.[1])
        .filter((value) => Boolean(value));
}
function matchesFindingTextSelector(finding, selector) {
    const query = selector.trim().toLowerCase();
    if (!query)
        return true;
    const id = finding.id.toLowerCase();
    const stableId = finding.stableId?.toLowerCase();
    const text = finding.text.toLowerCase();
    if (query.startsWith("fid:")) {
        const normalizedFid = query.slice(4).trim();
        if (!normalizedFid)
            return false;
        return stableId === normalizedFid || id === query || id === normalizedFid;
    }
    return id === query || stableId === query || text === query || text.includes(query);
}
/** Shared boilerplate for lifecycle mutation tools: validate project → call core fn → update index → map response. */
function withLifecycleMutation(phrenPath, project, writeQueue, updateIndex, handler, mapResponse) {
    if (!isValidProjectName(project))
        return mcpResponse({ ok: false, error: `Invalid project name: "${project}"` });
    return writeQueue(async () => {
        const result = handler();
        if (!result.ok)
            return mcpResponse({ ok: false, error: result.error });
        const resolvedFindingsDir = storeAwareProjectPath(phrenPath, project);
        if (resolvedFindingsDir)
            updateIndex(path.join(resolvedFindingsDir, FINDINGS_FILENAME));
        const mapped = mapResponse(result.data);
        return mcpResponse({ ok: true, message: mapped.message, data: mapped.data });
    });
}
// ── Handlers ─────────────────────────────────────────────────────────────────
async function handleAddFinding(ctx, params) {
    const { finding, sessionId, findingType, scope } = params;
    // `name` is the citation's code link (a function, type or variable);
    // `symbol` is its deprecated spelling, accepted until 0.3.1. The stored
    // citation keeps its existing key.
    const { name: citedName, ...citationRest } = params.citation ?? {};
    const citation = params.citation
        ? { ...citationRest, ...(citedName ?? citationRest.symbol ? { symbol: citedName ?? citationRest.symbol } : {}) }
        : undefined;
    // Resolve store-qualified project names (e.g., "team/arc" → store path + "arc")
    let phrenPath;
    let project;
    try {
        const resolved = resolveStoreForProject(ctx, params.project);
        phrenPath = resolved.phrenPath;
        project = resolved.project;
    }
    catch (err) {
        return mcpResponse({ ok: false, error: err instanceof Error ? err.message : String(err) });
    }
    const { withWriteQueue, updateFileInIndex } = ctx;
    if (!isValidProjectName(project))
        return mcpResponse({ ok: false, error: `Invalid project name: "${project}"` });
    const addFindingDenied = permissionDeniedError(phrenPath, "add_finding", project);
    if (addFindingDenied)
        return mcpResponse({ ok: false, error: addFindingDenied });
    const provenance = {
        source: "human",
        machine: getMachineName(),
        actor: getCurrentActor(),
        session_id: sessionId,
    };
    const normalizedScope = normalizeMemoryScope(scope ?? "shared");
    if (!normalizedScope)
        return mcpResponse({ ok: false, error: `Invalid scope: "${scope}". Use lowercase letters/numbers with '-' or '_' (max 64 chars), e.g. "researcher".` });
    // Size caps apply to every store; they used to sit after the team branch.
    const findingList = Array.isArray(finding) ? finding : [finding];
    if (findingList.length > 100)
        return mcpResponse({ ok: false, error: "Bulk add limited to 100 findings per call." });
    if (findingList.some((f) => f.length > 5000)) {
        return mcpResponse({
            ok: false,
            error: Array.isArray(finding) ? "One or more findings exceed 5000 character limit." : "Finding text exceeds 5000 character limit.",
        });
    }
    // Team stores: use append-only journal (no FINDINGS.md mutation, no merge conflicts)
    {
        const storeResolved = resolveStoreForProject(ctx, params.project);
        if (storeResolved.storeRole === "team") {
            const { appendTeamJournal } = await import("../finding/journal.js");
            // The journal is pushed to a repo shared with colleagues, so it gets the
            // same secret scan the personal store applies.
            const rejected = [];
            const accepted = [];
            for (const f of findingList) {
                const secretType = scanForSecrets(f);
                if (secretType)
                    rejected.push({ finding: f.slice(0, 60), reason: `Contains ${secretType}` });
                else
                    accepted.push(applyFindingTypePrefix(f, findingType));
            }
            return withWriteQueue(async () => {
                const added = [];
                const journals = new Set();
                for (const taggedFinding of accepted) {
                    const result = appendTeamJournal(phrenPath, project, taggedFinding, provenance.actor, provenance.machine);
                    if (result.ok) {
                        added.push(taggedFinding);
                        journals.add(path.join(phrenPath, project, "journal", result.data));
                    }
                    else {
                        rejected.push({ finding: taggedFinding.slice(0, 60), reason: result.error });
                    }
                }
                for (const journalPath of journals)
                    updateFileInIndex(journalPath);
                if (added.length === 0) {
                    return mcpResponse({
                        ok: false,
                        error: `No findings written to ${params.project} journal: ${rejected.map((r) => `"${r.finding}" ${r.reason}`).join("; ")}`,
                        data: { project: params.project, rejected, journalMode: true },
                    });
                }
                return mcpResponse({
                    ok: true,
                    message: `Added ${added.length} finding(s) to ${params.project} journal${rejected.length > 0 ? `, ${rejected.length} rejected` : ""}`,
                    data: { project: params.project, added, journalMode: true, ...(rejected.length > 0 ? { rejected } : {}) },
                });
            });
        }
    }
    if (Array.isArray(finding)) {
        const findings = finding;
        return withWriteQueue(async () => {
            runCustomHooks(phrenPath, "pre-finding", { PHREN_PROJECT: project });
            const allPotentialDuplicates = [];
            const allPotentialConflicts = [];
            const extraAnnotationsByFinding = [];
            for (const f of findings) {
                const candidates = findJaccardCandidates(phrenPath, project, f);
                if (candidates.length > 0)
                    allPotentialDuplicates.push({ finding: f, candidates });
                const conflictCandidates = findConflictCandidates(phrenPath, project, f);
                if (conflictCandidates.length > 0)
                    allPotentialConflicts.push({ finding: f, candidates: conflictCandidates });
                try {
                    const conflicts = await checkSemanticConflicts(phrenPath, project, f);
                    extraAnnotationsByFinding.push(conflicts.checked && conflicts.annotations.length > 0 ? conflicts.annotations : []);
                }
                catch (err) {
                    logger.debug("add_finding", `bulk semanticConflict: ${errorMessage(err)}`);
                    extraAnnotationsByFinding.push([]);
                }
            }
            const result = addFindingsToFile(phrenPath, project, findings, {
                extraAnnotationsByFinding,
                sessionId,
                scope: normalizedScope,
                provenance,
            });
            if (!result.ok)
                return mcpResponse({ ok: false, error: result.error });
            const { added, skipped, rejected } = result.data;
            if (added.length > 0) {
                runCustomHooks(phrenPath, "post-finding", { PHREN_PROJECT: project });
                incrementSessionFindings(phrenPath, added.length, sessionId, project);
                updateFileInIndex(path.join(phrenPath, project, FINDINGS_FILENAME));
            }
            const rejectedMsg = rejected.length > 0 ? `, ${rejected.length} rejected` : "";
            return mcpResponse({
                ok: true,
                message: `Added ${added.length}/${findings.length} findings (${skipped.length} duplicates skipped${rejectedMsg})`,
                data: {
                    project,
                    added,
                    skipped,
                    rejected,
                    ...(allPotentialDuplicates.length > 0 ? { potentialDuplicates: allPotentialDuplicates } : {}),
                    ...(allPotentialConflicts.length > 0 ? { potentialConflicts: allPotentialConflicts } : {}),
                },
            });
        });
    }
    return withWriteQueue(async () => {
        try {
            const taggedFinding = applyFindingTypePrefix(finding, findingType);
            // Memory link: link the finding to the one function, type or variable it
            // names, or validate an explicit citation `name`. Never rewrites the
            // finding text; only the citation comment gains the link.
            const code = moduleEnabled(phrenPath, "code") ? await loadCodePackage(phrenPath) : undefined;
            const symbolCitation = code ? await code.symbolCitationForFinding(phrenPath, project, taggedFinding, citation?.symbol) : citation?.symbol ? { symbol: citation.symbol } : {};
            const citationForWrite = (citation || symbolCitation.symbol)
                ? { ...(citation ?? {}), ...symbolCitation }
                : undefined;
            // Jaccard "maybe zone" scan — free, no LLM call. Return candidates so the agent decides.
            const potentialDuplicates = findJaccardCandidates(phrenPath, project, taggedFinding);
            // Heuristic contradiction candidates — also free, also agent-decides. No extra API call.
            const potentialConflicts = findConflictCandidates(phrenPath, project, taggedFinding);
            const semanticConflicts = await checkSemanticConflicts(phrenPath, project, taggedFinding);
            runCustomHooks(phrenPath, "pre-finding", { PHREN_PROJECT: project });
            const result = addFindingToFile(phrenPath, project, taggedFinding, citationForWrite, {
                sessionId,
                scope: normalizedScope,
                extraAnnotations: semanticConflicts.checked ? semanticConflicts.annotations : undefined,
                provenance,
            });
            if (!result.ok) {
                return mcpResponse({ ok: false, error: result.error });
            }
            if (result.data.status === "skipped") {
                return mcpResponse({ ok: true, message: result.data.message, data: { project, finding: taggedFinding, status: "skipped" } });
            }
            updateFileInIndex(path.join(phrenPath, project, FINDINGS_FILENAME));
            if (result.data.status === "added" || result.data.status === "created") {
                runCustomHooks(phrenPath, "post-finding", { PHREN_PROJECT: project });
                incrementSessionFindings(phrenPath, 1, sessionId, project);
                extractFactFromFinding(phrenPath, project, taggedFinding);
                // Bidirectional link: if there's an active task in this session, append this finding to it.
                if (sessionId) {
                    const activeTask = getActiveTaskForSession(phrenPath, sessionId, project);
                    if (activeTask) {
                        const taskMatch = activeTask.stableId ? `bid:${activeTask.stableId}` : activeTask.line;
                        // Extract fid from the last written line in FINDINGS.md
                        try {
                            const findingsPath = path.join(phrenPath, project, FINDINGS_FILENAME);
                            const findingsContent = fs.readFileSync(findingsPath, "utf8");
                            const lines = findingsContent.split("\n");
                            const taggedText = taggedFinding.replace(/^-\s+/, "").trim().slice(0, 60).toLowerCase();
                            for (let li = lines.length - 1; li >= 0; li--) {
                                const l = lines[li];
                                if (!l.startsWith("- "))
                                    continue;
                                const lineText = l.replace(/<!--.*?-->/g, "").replace(/^-\s+/, "").trim().slice(0, 60).toLowerCase();
                                if (lineText === taggedText || l.toLowerCase().includes(taggedText.slice(0, 30))) {
                                    const fidMatch = l.match(/<!--\s*fid:([a-z0-9]{8})\s*-->/);
                                    if (fidMatch) {
                                        appendChildFinding(phrenPath, project, taskMatch, `fid:${fidMatch[1]}`);
                                    }
                                    break;
                                }
                            }
                        }
                        catch {
                            // Non-fatal: task-finding linkage is best-effort
                        }
                    }
                }
            }
            const conflictsWithList = semanticConflicts.checked
                ? extractConflictsWith(semanticConflicts.annotations)
                : (result.data.message.match(/<!--\s*conflicts_with:\s*"([^"]+)"/)?.[1] ? [result.data.message.match(/<!--\s*conflicts_with:\s*"([^"]+)"/)[1]] : []);
            const conflictsWith = conflictsWithList[0];
            // Extract fragment hints synchronously from the finding text (regex only, no DB).
            // Full DB fragment linking happens on the next index rebuild via updateFileInIndex →
            // extractAndLinkFragments. We surface hints here so callers can see what was detected.
            const detectedFragments = extractFragmentNames(taggedFinding);
            // Surface heuristic conflict candidates for the agent to judge (only when the LLM path
            // didn't already confirm a conflict, to avoid double-reporting the same relationship).
            const conflictNote = (potentialConflicts.length > 0 && conflictsWithList.length === 0)
                ? ` ⚠ Possible contradiction with existing finding(s): ${potentialConflicts.map((c) => `"${c}"`).join("; ")}.` +
                    ` If this genuinely contradicts one, resolve it with resolve_contradiction (or supersede_finding); if they're unrelated, ignore this note.`
                : "";
            return mcpResponse({
                ok: true,
                message: result.data.message + conflictNote,
                data: {
                    project,
                    finding: taggedFinding,
                    status: result.data.status,
                    ...(conflictsWith ? { conflictsWith } : {}),
                    ...(conflictsWithList.length > 0 ? { conflicts: conflictsWithList } : {}),
                    ...(detectedFragments.length > 0 ? { detectedFragments } : {}),
                    ...(potentialDuplicates.length > 0 ? { potentialDuplicates } : {}),
                    ...(potentialConflicts.length > 0 ? { potentialConflicts } : {}),
                    scope: normalizedScope,
                }
            });
        }
        catch (err) {
            if (err instanceof Error && err.message.includes("Rejected:")) {
                return mcpResponse({ ok: false, error: errorMessage(err), errorCode: "VALIDATION_ERROR" });
            }
            return mcpResponse({ ok: false, error: `Unexpected error saving finding: ${errorMessage(err)}` });
        }
    });
}
async function handleSupersedeFinding(ctx, { project: projectInput, finding_text, superseded_by }) {
    let phrenPath;
    let project;
    try {
        const resolved = resolveStoreForProject(ctx, projectInput);
        phrenPath = resolved.phrenPath;
        project = resolved.project;
    }
    catch (err) {
        return mcpResponse({ ok: false, error: err instanceof Error ? err.message : String(err) });
    }
    const { withWriteQueue, updateFileInIndex } = ctx;
    return withLifecycleMutation(phrenPath, project, withWriteQueue, updateFileInIndex, () => supersedeFinding(phrenPath, project, finding_text, superseded_by), (data) => ({
        message: `Marked finding as superseded in ${project}.`,
        data: { project, finding: data.finding, status: data.status, superseded_by: data.superseded_by },
    }));
}
async function handleRetractFinding(ctx, { project: projectInput, finding_text, reason }) {
    let phrenPath;
    let project;
    try {
        const resolved = resolveStoreForProject(ctx, projectInput);
        phrenPath = resolved.phrenPath;
        project = resolved.project;
    }
    catch (err) {
        return mcpResponse({ ok: false, error: err instanceof Error ? err.message : String(err) });
    }
    const { withWriteQueue, updateFileInIndex } = ctx;
    return withLifecycleMutation(phrenPath, project, withWriteQueue, updateFileInIndex, () => retractFindingLifecycle(phrenPath, project, finding_text, reason), (data) => ({
        message: `Retracted finding in ${project}.`,
        data: { project, finding: data.finding, status: data.status, reason: data.reason },
    }));
}
async function handleResolveContradiction(ctx, { project: projectInput, finding_text, finding_text_other, finding_a, finding_b, resolution }) {
    let phrenPath;
    let project;
    try {
        const resolved = resolveStoreForProject(ctx, projectInput);
        phrenPath = resolved.phrenPath;
        project = resolved.project;
    }
    catch (err) {
        return mcpResponse({ ok: false, error: err instanceof Error ? err.message : String(err) });
    }
    const { withWriteQueue, updateFileInIndex } = ctx;
    const findingText = (finding_text ?? finding_a)?.trim();
    const findingTextOther = (finding_text_other ?? finding_b)?.trim();
    if (!findingText || !findingTextOther) {
        return mcpResponse({
            ok: false,
            error: "Both finding_text and finding_text_other are required.",
        });
    }
    return withLifecycleMutation(phrenPath, project, withWriteQueue, updateFileInIndex, () => resolveFindingContradiction(phrenPath, project, findingText, findingTextOther, resolution), (data) => ({
        message: `Resolved contradiction in ${project} with "${resolution}".`,
        data: {
            project,
            resolution: data.resolution,
            finding_text: data.finding_a,
            finding_text_other: data.finding_b,
            finding_a: data.finding_a,
            finding_b: data.finding_b,
        },
    }));
}
async function handleGetContradictions(ctx, { project, finding_text }) {
    if (project && !isValidProjectName(project))
        return mcpResponse({ ok: false, error: `Invalid project name: "${project}"` });
    // Build project list from all stores (primary + team)
    let projectsWithPaths;
    if (project) {
        const resolved = resolveStoreForProject(ctx, project, "read");
        projectsWithPaths = [{ project: resolved.project, storePath: resolved.phrenPath }];
    }
    else {
        const { listAllProjects } = await import("../store-routing.js");
        projectsWithPaths = listAllProjects(ctx.phrenPath, ctx.profile)
            .map((p) => ({ project: p.projectName, storePath: p.store.path }));
    }
    const contradictions = [];
    for (const { project: p, storePath } of projectsWithPaths) {
        const result = readFindings(storePath, p);
        if (!result.ok)
            continue;
        for (const finding of result.data) {
            if (finding.status !== "contradicted")
                continue;
            if (finding_text && !matchesFindingTextSelector(finding, finding_text))
                continue;
            contradictions.push({
                project: p,
                id: finding.id,
                stableId: finding.stableId,
                text: finding.text,
                date: finding.date,
                status_updated: finding.status_updated,
                status_reason: finding.status_reason,
                status_ref: finding.status_ref,
            });
        }
    }
    return mcpResponse({
        ok: true,
        message: contradictions.length
            ? `Found ${contradictions.length} unresolved contradiction${contradictions.length === 1 ? "" : "s"}.`
            : "No unresolved contradictions found.",
        data: {
            project: project ?? null,
            finding_text: finding_text ?? null,
            contradictions,
        },
    });
}
async function handleEditFinding(ctx, { project: projectInput, old_text, new_text }) {
    let phrenPath;
    let project;
    try {
        const resolved = resolveStoreForProject(ctx, projectInput);
        phrenPath = resolved.phrenPath;
        project = resolved.project;
    }
    catch (err) {
        return mcpResponse({ ok: false, error: err instanceof Error ? err.message : String(err) });
    }
    const { withWriteQueue, updateFileInIndex } = ctx;
    if (!isValidProjectName(project))
        return mcpResponse({ ok: false, error: `Invalid project name: "${project}"` });
    const editDenied = permissionDeniedError(phrenPath, "edit_finding", project);
    if (editDenied)
        return mcpResponse({ ok: false, error: editDenied });
    return withWriteQueue(async () => {
        const result = editFindingCore(phrenPath, project, old_text, new_text);
        if (!result.ok)
            return mcpResponse({ ok: false, error: result.error });
        const resolvedFindingsDir = storeAwareProjectPath(phrenPath, project);
        if (resolvedFindingsDir)
            updateFileInIndex(path.join(resolvedFindingsDir, FINDINGS_FILENAME));
        return mcpResponse({
            ok: true,
            message: result.data,
            data: { project, old_text, new_text },
        });
    });
}
async function handleRemoveFinding(ctx, { project: projectInput, finding }) {
    let phrenPath;
    let project;
    try {
        const resolved = resolveStoreForProject(ctx, projectInput);
        phrenPath = resolved.phrenPath;
        project = resolved.project;
    }
    catch (err) {
        return mcpResponse({ ok: false, error: err instanceof Error ? err.message : String(err) });
    }
    const { withWriteQueue, updateFileInIndex } = ctx;
    if (!isValidProjectName(project))
        return mcpResponse({ ok: false, error: `Invalid project name: "${project}"` });
    const removeDenied = permissionDeniedError(phrenPath, "remove_finding", project);
    if (removeDenied)
        return mcpResponse({ ok: false, error: removeDenied });
    if (Array.isArray(finding)) {
        return withWriteQueue(async () => {
            const result = removeFindingsCore(phrenPath, project, finding);
            if (!result.ok)
                return mcpResponse({ ok: false, error: result.message });
            const resolvedFindingsDir = storeAwareProjectPath(phrenPath, project);
            if (resolvedFindingsDir)
                updateFileInIndex(path.join(resolvedFindingsDir, FINDINGS_FILENAME));
            return mcpResponse({ ok: true, message: result.message, data: result.data });
        });
    }
    return withWriteQueue(async () => {
        const result = removeFindingCore(phrenPath, project, finding);
        if (!result.ok)
            return mcpResponse({ ok: false, error: result.message });
        const resolvedFindingsDir = storeAwareProjectPath(phrenPath, project);
        if (resolvedFindingsDir)
            updateFileInIndex(path.join(resolvedFindingsDir, FINDINGS_FILENAME));
        return mcpResponse({ ok: true, message: result.message, data: result.data });
    });
}
/**
 * Commit and push the team-safe pathspecs of every attached team store. Team
 * stores are independent repos, so push_changes runs this whatever happens to
 * the primary store.
 */
export async function syncTeamStores(phrenPath) {
    const teamResults = [];
    try {
        const { execFileSync } = await import("child_process");
        const { getNonPrimaryStores } = await import("../store-registry.js");
        const teamStores = getNonPrimaryStores(phrenPath).filter((s) => s.role === "team");
        for (const store of teamStores) {
            if (!fs.existsSync(store.path) || !fs.existsSync(path.join(store.path, ".git")))
                continue;
            const runStoreGit = (args, opts = {}) => execFileSync("git", args, {
                cwd: store.path,
                encoding: "utf8",
                timeout: opts.timeout ?? EXEC_TIMEOUT_MS,
                env: nonInteractiveGitEnv(opts.env),
                stdio: ["ignore", "pipe", "pipe"],
            }).trim();
            const mergeStoreGit = async (_cwd, gitArgs) => {
                try {
                    return { ok: true, output: runStoreGit(gitArgs) };
                }
                catch (err) {
                    return { ok: false, output: "", error: errorMessage(err) };
                }
            };
            try {
                if (!runStoreGit(["status", "--porcelain"]))
                    continue;
                // Stage each team-safe pathspec individually — a single no-match
                // (e.g. no */truths.md in this store) used to abort the whole add.
                for (const spec of TEAM_STORE_PATHSPECS) {
                    try {
                        runStoreGit(["add", "--sparse", "--", spec]);
                    }
                    catch { /* best-effort */ }
                }
                if (!runStoreGit(["diff", "--cached", "--name-only"]))
                    continue;
                const actor = process.env.PHREN_ACTOR || process.env.USER || "unknown";
                runStoreGit(["commit", "-m", storeCommitMessage(`phren: ${actor} team sync`)]);
                try {
                    runStoreGit(["push"], { timeout: 15000 });
                    teamResults.push({ store: store.name, pushed: true });
                }
                catch {
                    try {
                        const merged = await mergeStoreUpstream(store.path, { git: mergeStoreGit, commitLocalWrites: false });
                        if (merged.status !== "updated" && merged.status !== "unchanged")
                            throw new Error(merged.detail);
                        runStoreGit(["push"], { timeout: 15000 });
                        teamResults.push({ store: store.name, pushed: true });
                    }
                    catch (retryErr) {
                        teamResults.push({ store: store.name, pushed: false, error: errorMessage(retryErr) });
                    }
                }
            }
            catch (storeErr) {
                teamResults.push({ store: store.name, pushed: false, error: errorMessage(storeErr) });
            }
        }
    }
    catch (err) {
        debugLog(`syncTeamStores: ${errorMessage(err)}`);
    }
    return teamResults;
}
/** Team-store outcomes appended to a push_changes message, so a failure is visible. */
function describeTeamSync(results) {
    if (results.length === 0)
        return "";
    const pushed = results.filter((r) => r.pushed).map((r) => r.store);
    const parts = pushed.length > 0 ? [`Pushed ${pushed.length} team store(s): ${pushed.join(", ")}.`] : [];
    for (const failure of results.filter((r) => !r.pushed))
        parts.push(`Team store "${failure.store}" failed: ${failure.error ?? "unknown error"}.`);
    return ` ${parts.join(" ")}`;
}
async function handlePushChanges(ctx, { message }) {
    const { phrenPath, withWriteQueue } = ctx;
    return withWriteQueue(async () => withFileLock(runtimeFile(phrenPath, "git-op"), async () => {
        const { execFileSync } = await import("child_process");
        const runGit = (args, opts = {}) => execFileSync("git", args, {
            cwd: phrenPath,
            encoding: "utf8",
            timeout: opts.timeout ?? EXEC_TIMEOUT_MS,
            env: nonInteractiveGitEnv(opts.env),
            stdio: ["ignore", "pipe", "pipe"],
        }).trim();
        const mergeGit = async (_cwd, args) => {
            try {
                return { ok: true, output: runGit(args) };
            }
            catch (err) {
                return { ok: false, output: "", error: errorMessage(err) };
            }
        };
        const teamResults = await syncTeamStores(phrenPath);
        const teamSuffix = describeTeamSync(teamResults);
        const teamData = teamResults.length > 0 ? { teamStores: teamResults } : {};
        try {
            const status = runGit(["status", "--porcelain"]);
            if (!status)
                return mcpResponse({ ok: true, message: `Nothing to save. Phren is up to date.${teamSuffix}`, data: { files: 0, pushed: false, ...teamData } });
            const files = status.split("\n").filter(Boolean);
            const projectNames = Array.from(new Set(files
                .map((line) => line.slice(3).trim().split("/")[0])
                .filter((name) => name && !name.startsWith(".") && name !== "profiles")));
            const commitMsg = message || `phren: save ${files.length} file(s) across ${projectNames.length} project(s)`;
            runCustomHooks(phrenPath, "pre-save");
            // Stage all files including untracked (new project dirs, first FINDINGS.md, etc.)
            runGit(["add", "--sparse", "-A"]);
            // Belt-and-suspenders: unstage sensitive files that .gitignore should
            // already block (mirrors the same defensive reset in cli/session-stop.ts's
            // auto-save). .config/auth-profiles.json is the legacy path for
            // auth/profiles.ts's credential store (API keys, OpenAI Codex OAuth
            // tokens) — this catches a store where the file was already tracked
            // before it was gitignored, so a later token refresh doesn't get
            // re-staged and pushed. Failures here are non-fatal (files may not exist).
            try {
                runGit(["reset", "HEAD", "--", ".env", "**/.env", "*.pem", "*.key", ".config/auth-profiles.json"]);
            }
            catch { /* best effort */ }
            runGit(["commit", "-m", storeCommitMessage(commitMsg)]);
            let hasRemote = false;
            try {
                const remotes = runGit(["remote"]);
                hasRemote = remotes.length > 0;
            }
            catch (err) {
                logger.warn("push_changes", `remoteCheck: ${errorMessage(err)}`);
            }
            if (!hasRemote) {
                const changedFiles = status.split("\n").filter(Boolean).length;
                return mcpResponse({ ok: true, message: `Saved ${changedFiles} changed file(s). No remote configured, skipping push.${teamSuffix}`, data: { files: changedFiles, pushed: false, ...teamData } });
            }
            let pushed = false;
            let lastPushError = "";
            const delays = [2000, 4000, 8000];
            for (let attempt = 0; attempt <= 3; attempt++) {
                try {
                    runGit(["push"], { timeout: 15000 });
                    pushed = true;
                    break;
                }
                catch (pushErr) {
                    lastPushError = pushErr instanceof Error ? pushErr.message : String(pushErr);
                    debugLog(`Push attempt ${attempt + 1} failed: ${lastPushError}`);
                    if (attempt < 3) {
                        const merged = await mergeStoreUpstream(phrenPath, { git: mergeGit, commitLocalWrites: false });
                        if (merged.status !== "updated" && merged.status !== "unchanged") {
                            logger.warn("push_changes", `mergeRemote: ${merged.detail}`);
                            break;
                        }
                        await new Promise(r => setTimeout(r, delays[attempt]));
                    }
                }
            }
            const changedFiles = status.split("\n").filter(Boolean).length;
            runCustomHooks(phrenPath, "post-save", { PHREN_FILES_CHANGED: String(changedFiles), PHREN_PUSHED: String(pushed) });
            if (pushed) {
                return mcpResponse({ ok: true, message: `Saved ${changedFiles} changed file(s). Pushed to remote.${teamSuffix}`, data: { files: changedFiles, pushed: true, ...teamData } });
            }
            else {
                return mcpResponse({
                    ok: true,
                    message: `Changes were committed but push failed.\n\nGit error: ${lastPushError}\n\nRun 'git push' manually from your phren directory.${teamSuffix}`,
                    data: { files: changedFiles, pushed: false, pushError: lastPushError, ...teamData },
                });
            }
        }
        catch (err) {
            return mcpResponse({ ok: false, error: `Save failed: ${errorMessage(err)}${teamSuffix}`, errorCode: "INTERNAL_ERROR" });
        }
    }));
}
// ── Registration ─────────────────────────────────────────────────────────────
export function register(server, ctx) {
    server.registerTool("add_finding", {
        title: "◆ phren · save finding",
        description: "Tell phren one or more insights for a project's FINDINGS.md. Call this the moment you discover " +
            "a non-obvious pattern, hit a subtle bug, find a workaround, or learn something that would " +
            "save time in a future session. Do not wait until the end of the session." +
            " Pass a single string or an array of strings." +
            " Optionally classify with findingType: decision, pitfall, pattern, tradeoff, architecture, or bug.",
        inputSchema: z.object({
            project: z.string().describe("Project name (must match a directory in your phren store)."),
            finding: z.preprocess((v) => (typeof v === "string" ? [v] : v), z.array(z.string()).min(1)).describe("The insight(s) to save. Always pass as an array of strings — use a single-element array for one finding."),
            citation: z.object({
                file: z.string().optional().describe("Source file path that supports this finding."),
                line: z.number().int().positive().optional().describe("1-based line number in file."),
                repo: z.string().optional().describe("Git repository root path for citation validation."),
                commit: z.string().optional().describe("Git commit SHA that supports this finding."),
                name: z.string().optional().describe("The function, type or variable this finding is about: Name, Type.member or name(). Validated against the project's code index; stored unresolved when it does not resolve."),
                symbol: z.string().optional().describe("Deprecated: use name. Accepted until @phren/cli 0.3.1."),
                supersedes: z.string().optional().describe("First 60 chars of the old finding this one replaces. The old entry will be marked as superseded."),
                task_item: z.string().optional().describe("Task item stable ID like bid:abcd1234, positional ID like A1, or item text to link this finding to."),
            }).optional().describe("Optional source citation for traceability (only used when finding is a single string)."),
            sessionId: z.string().optional().describe("Optional session ID from session_start. Pass this if you want session metrics to include this write."),
            findingType: z.enum(FINDING_TYPES)
                .optional()
                .describe("Classify this finding: 'decision' (architectural choice with rationale), 'pitfall' (bug or failure mode to avoid), 'pattern' (reusable approach that works well), 'bug' (confirmed defect or failure)."),
            scope: z.string().optional().describe("Optional memory scope label. Defaults to 'shared'. Example: 'researcher' or 'builder'."),
        }),
    }, (params) => handleAddFinding(ctx, params));
    server.registerTool("supersede_finding", {
        title: "◆ phren · supersede finding",
        description: "Mark an existing finding as superseded and link it to the newer finding text.",
        inputSchema: z.object({
            project: z.string().describe("Project name."),
            finding_text: z.string().describe("Finding to supersede (supports fid, exact text, or partial match)."),
            superseded_by: z.string().describe("Text of the new finding that supersedes this one."),
        }),
    }, (params) => handleSupersedeFinding(ctx, params));
    server.registerTool("retract_finding", {
        title: "◆ phren · retract finding",
        description: "Mark an existing finding as retracted and store the reason in lifecycle metadata.",
        inputSchema: z.object({
            project: z.string().describe("Project name."),
            finding_text: z.string().describe("Finding to retract (supports fid, exact text, or partial match)."),
            reason: z.string().describe("Reason for retraction."),
        }),
    }, (params) => handleRetractFinding(ctx, params));
    server.registerTool("resolve_contradiction", {
        title: "◆ phren · resolve contradiction",
        description: "Resolve a contradiction between two findings and update lifecycle status based on the chosen resolution.",
        inputSchema: z.object({
            project: z.string().describe("Project name."),
            finding_text: z.string().optional().describe("First finding (supports fid, exact text, or partial match)."),
            finding_text_other: z.string().optional().describe("Second finding (supports fid, exact text, or partial match)."),
            finding_a: z.string().optional().describe("Deprecated alias for finding_text."),
            finding_b: z.string().optional().describe("Deprecated alias for finding_text_other."),
            resolution: z.enum(["keep_a", "keep_b", "keep_both", "retract_both"]).describe("Resolution strategy."),
        }).superRefine((value, zodCtx) => {
            if (!(value.finding_text ?? value.finding_a)) {
                zodCtx.addIssue({
                    code: z.ZodIssueCode.custom,
                    path: ["finding_text"],
                    message: "finding_text is required.",
                });
            }
            if (!(value.finding_text_other ?? value.finding_b)) {
                zodCtx.addIssue({
                    code: z.ZodIssueCode.custom,
                    path: ["finding_text_other"],
                    message: "finding_text_other is required.",
                });
            }
        }),
    }, (params) => handleResolveContradiction(ctx, params));
    server.registerTool("get_contradictions", {
        title: "◆ phren · contradictions",
        description: "List unresolved contradictions (findings currently marked with status contradicted).",
        inputSchema: z.object({
            project: z.string().optional().describe("Optional project filter. When omitted, scans all projects."),
            finding_text: z.string().optional().describe("Optional finding selector (supports fid, exact text, or partial match)."),
        }),
    }, (params) => handleGetContradictions(ctx, params));
    server.registerTool("edit_finding", {
        title: "◆ phren · edit finding",
        description: "Edit a finding in place while preserving its metadata and history.",
        inputSchema: z.object({
            project: z.string().describe("Project name."),
            old_text: z.string().describe("Existing finding text to match."),
            new_text: z.string().describe("Replacement finding text."),
        }),
    }, (params) => handleEditFinding(ctx, params));
    server.registerTool("remove_finding", {
        title: "◆ phren · remove finding",
        description: "Remove one or more findings from a project's FINDINGS.md by matching text. Use this when a " +
            "previously captured insight turns out to be wrong, outdated, or no longer relevant." +
            " Pass a single string or an array of strings.",
        inputSchema: z.object({
            project: z.string().describe("Project name."),
            finding: z.preprocess((v) => (typeof v === "string" ? [v] : v), z.array(z.string()).min(1)).describe("Text(s) to match and remove. Always pass as an array of strings — use a single-element array for one."),
        }),
    }, (params) => handleRemoveFinding(ctx, params));
    server.registerTool("push_changes", {
        title: "◆ phren · push",
        description: "Commit and push any changes in the phren store. Call this at the end of a session " +
            "or after adding multiple findings/tasks items. Commits all modified files in the " +
            "phren directory and pushes if a remote is configured.",
        inputSchema: z.object({
            message: z.string().optional().describe("Commit message. Defaults to 'update phren'."),
        }),
    }, (params) => handlePushChanges(ctx, params));
}