studiograph 1.3.48-next.2 → 1.3.48-next.201

package/dist/core/graph.d.ts

@@ -6,10 +6,13 @@
  */
 import { GitService, GitUser } from '../services/git.js';
 import { MarkdownDocument } from '../services/markdown.js';
-import { AssetInfo, AssetConfig } from '../services/assets/index.js';
+import type { BodyWriteCoordinator, BodyWriteResult } from '../server/body-write-coordinator.js';
+import { AssetService, AssetInfo, AssetRecord, AssetConfig, type AssetUploadResult } from '../services/assets/index.js';
+import type { AssetIndexService } from '../services/assets/asset-index-service.js';
 import { EntityType, type EntityData, type DatasetRow } from './validation.js';
 import { SchemaRegistry } from './schema-registry.js';
 import { type DatasetFilter } from '../services/csv-service.js';
+import { type HistoryCommitChange } from './history-diff.js';
 import { type VectorService } from '../services/vector-service.js';
 export interface GraphConfig {
     repoPath: string;
@@ -20,14 +23,38 @@ export interface GraphConfig {
     schemaRegistry?: SchemaRegistry;
     /** When true, all git operations are skipped. Used for the private/ graph. */
     noGit?: boolean;
+    /** Workspace root path. Used to anchor cross-repo artefacts like the
+     *  PDF text sidecar at `<workspaceRoot>/.studiograph/assets-text/...`.
+     *  Optional — when undefined, sidecar cleanup is a no-op. */
+    workspaceRoot?: string;
 }
 export interface EntityFile {
     id: string;
     path: string;
+    /** Repo-relative POSIX path of the containing folder. "" for repo root. */
+    folder_path: string;
     entityType: string;
     data: EntityData;
     document: MarkdownDocument;
 }
+export interface FolderEntry {
+    /** Repo-relative POSIX path. */
+    path: string;
+    /** Last segment of the path. */
+    name: string;
+    /** Optional human-readable label. Set only when an explicit override exists
+     *  in the folder's `.studiograph-folder.json` sidecar; clients fall back to
+     *  toDisplayName(name) when undefined. */
+    display_name?: string;
+    /** Stable folder id from the sidecar, when assigned. Eagerly written on
+     *  folder creation; absent for folders never mutated through the app (those
+     *  fall back to a path-based scope key). Reads never generate one. */
+    id?: string;
+}
+export interface FolderDeleteResult {
+    entriesDeleted: number;
+    subfoldersDeleted: number;
+}
 export interface SearchOptions {
     entityType?: EntityType;
     query?: string;
@@ -40,6 +67,12 @@ export interface SearchOptions {
     };
     sortBy?: 'created_at' | 'updated_at' | 'relevance';
     limit?: number;
+    /**
+     * When true, score only on name match — skip frontmatter field scan and
+     * full-body content scan. Used by autosuggest, where scanning every
+     * entity's markdown body dominates wall time.
+     */
+    nameOnly?: boolean;
 }
 export interface CreateEntityOptions {
     entityType: EntityType;
@@ -48,9 +81,39 @@ export interface CreateEntityOptions {
     content?: string;
     commitMessage?: string;
     skipCommit?: boolean;
+    /**
+     * Repo-relative folder to create the entry in. Empty/undefined = repo root.
+     * Parent folders are auto-created (mkdir -p semantics).
+     */
+    folderPath?: string;
     /** Override commit author (for per-user attribution in web UI). */
     user?: GitUser;
+    /**
+     * Suppress the fire-and-forget vector upsert for THIS create. Used by the
+     * asset-upload flow, where the entity is created as a `__pending__` stub
+     * (no sidecar, no `indexable`) and then finalized by a follow-up `update`.
+     * Indexing the stub is both wasteful (name-only, pre-sidecar) and racy: its
+     * async embedding can resolve AFTER the finalizing update's body-inclusive
+     * upsert and clobber the good row, leaving the asset searchable by filename
+     * only. Skipping it means the single authoritative upsert is the finalizing
+     * update, after the sidecar is on disk. Default false (every other path
+     * indexes on create as before).
+     */
+    skipVectorIndex?: boolean;
 }
+/**
+ * Body-write provenance. Every `graph.update` call that passes `content`
+ * must declare its `source`.
+ *
+ * - `'autosave'`: web editor autosave PUT. Content came from a live Y.Text;
+ *   the live Y.Doc is already authoritative, so we write disk + commit
+ *   under the per-doc lock but do NOT re-apply to the Y.Doc (that would
+ *   race in-flight keystrokes typed during the round trip).
+ * - `'server-write'`: any server-side caller (MCP `update_entity`, agent
+ *   tools, event processor). Routes through `applyAgentContent` under the
+ *   per-doc lock so live editors receive the broadcast post-commit.
+ */
+export type BodyWriteSource = 'autosave' | 'server-write';
 export interface UpdateEntityOptions {
     entityType: EntityType;
     entityId: string;
@@ -60,6 +123,98 @@ export interface UpdateEntityOptions {
     skipCommit?: boolean;
     /** Override commit author (for per-user attribution in web UI). */
     user?: GitUser;
+    /**
+     * Required when `content !== undefined`. See {@link BodyWriteSource}.
+     */
+    source?: BodyWriteSource;
+    /**
+     * Optional precondition for body writes. When set, the server compares
+     * this hash to `sha256(existing.document.content)` BEFORE mutating
+     * anything. Mismatch throws {@link StaleBaseRevisionError} so the caller
+     * can refetch + recompute. When omitted, last-writer-wins.
+     *
+     * Content hash, not `updated_at`, because two `new Date().toISOString()`
+     * stamps can alias to the same millisecond on fast hardware.
+     */
+    baseRevision?: string;
+    /**
+     * Optional sink for the body-write broadcast disposition. Only fires on
+     * the coordinator (body-write) path. Lets a caller (e.g. MCP
+     * update_entity) surface `broadcast-failed` in its diagnostics instead
+     * of the disposition being discarded after `writeBody` returns.
+     */
+    onBroadcast?: (disposition: BodyWriteResult['broadcast']) => void;
+}
+/**
+ * Thrown by `graph.update` when the git commit fails after the disk write
+ * has already landed. The .md is updated and observable to subsequent
+ * readers via `graph.get`, but no commit exists — the repo is dirty.
+ *
+ * The caller MUST surface this typed error so an operator can recover
+ * (manual `git add && git commit`, or `git checkout -- <path>` to revert
+ * disk). v3-of-the-plan claim of "auto-convergence via sessionManager"
+ * was false outside the autosave PUT path; Phase 2 explicitly registers
+ * server-side dirty files with sessionManager when available, but the
+ * caller still gets the typed error so it knows the write was partial.
+ */
+export declare class CommitFailedDirtyError extends Error {
+    readonly entityType: string;
+    readonly entityId: string;
+    readonly path: string;
+    readonly code: "COMMIT_FAILED_DIRTY";
+    constructor(entityType: string, entityId: string, path: string, cause: unknown);
+}
+/**
+ * Thrown by `graph.update` when a body write supplies a `baseRevision`
+ * that doesn't match the current body's content hash. Caller (autosave,
+ * MCP, agent, event processor) refetches and retries against the new
+ * revision.
+ */
+export declare class StaleBaseRevisionError extends Error {
+    readonly entityType: string;
+    readonly entityId: string;
+    readonly expected: string;
+    readonly actual: string;
+    readonly code: "STALE_BASE_REVISION";
+    constructor(entityType: string, entityId: string, expected: string, actual: string);
+}
+/**
+ * Callbacks that fire AFTER successful structural mutations. Used by the Yjs
+ * persistence layer so snapshot files follow the .md file (rename → rename
+ * snapshot, delete → delete snapshot, type change → rename across type dirs).
+ *
+ * Hooked at this layer because the four mutation methods (delete, rename,
+ * changeType, plus cross-repo create+delete via /transfer) are the canonical
+ * mutation surface — every code path that moves an entity goes through them.
+ *
+ * Body-write hooks (onBodyWritten, applyAgentContent, withDocLock,
+ * assertWritable, onCommitFailedDirty) used to live here too. Phase 4
+ * extracted them into {@link BodyWriteCoordinator} — different concurrency
+ * profile, single critical section. This interface now covers ONLY the
+ * structural-mutation notifications that drive snapshot bookkeeping.
+ */
+export interface GraphPersistenceCallbacks {
+    onDelete?(repo: string, entityType: string, entityId: string): void | Promise<void>;
+    onRename?(repo: string, entityType: string, oldId: string, newId: string): void | Promise<void>;
+    onChangeType?(repo: string, entityId: string, fromType: string, toType: string): void | Promise<void>;
+}
+/**
+ * Thrown by `restoreFile` when the path the recreate would land at is
+ * currently occupied by a different entity. Carries the occupant's
+ * coordinates so callers (agent tool, REST endpoint) can surface a
+ * useful error to the user.
+ */
+export declare class PathConflictError extends Error {
+    readonly path: string;
+    readonly occupiedBy: {
+        entityType: string;
+        entityId: string;
+    };
+    readonly code: "PATH_CONFLICT";
+    constructor(path: string, occupiedBy: {
+        entityType: string;
+        entityId: string;
+    });
 }
 export declare class BaseGraphManager {
     private repoPath;
@@ -67,22 +222,151 @@ export declare class BaseGraphManager {
     private gitService?;
     private noGit;
     private markdownService;
+    private csvService;
     private assetService?;
+    /** Workspace-global ownership index for immutable-keyed assets. Injected by
+     *  WorkspaceManager (one per workspace). Undefined in coordinator-less test
+     *  / CLI graphs — those fall back to the legacy `{type}/{id}` key scheme. */
+    private assetIndex?;
     private gitUser;
-    private csvService;
     private vectorService?;
     private schemaRegistry?;
+    private workspaceRoot?;
+    /** Cache for history-panel change summaries, keyed by `${relPath}@${hash}`.
+     *  A commit's diff against its parent is immutable, so this never needs
+     *  invalidation — entries only accumulate as history is viewed. */
+    private historyChangeCache;
+    private persistenceCallbacks?;
+    private bodyWriteCoordinator?;
     constructor(config: GraphConfig);
-    /** Expose git service for deferred commit operations (e.g. CommitScheduler). */
+    /**
+     * Friendly display label for an entity type — custom-type label when the
+     * workspace defines one, otherwise the title-cased key ("deal" → "Deal").
+     * Used to build human-readable commit messages.
+     */
+    private typeLabel;
+    /** Build an EntityRef for a commit message from a type, id, and optional title. */
+    private commitRef;
+    /**
+     * Build the friendly "Edited …" message for a deferred (batched) commit,
+     * given the "type/id" pairs accumulated by the SessionManager. Each title is
+     * resolved from the in-memory index at flush time (cheap lookup); an entity
+     * deleted before the flush falls back to its slug id.
+     */
+    buildEditedBatchMessage(entities: Array<{
+        type: string;
+        id: string;
+    }>): string;
+    /**
+     * Change summary for one commit in a file's history — which frontmatter
+     * fields moved and whether the body changed — by diffing the file at `hash`
+     * against its true git parent (`hash^`). Used by the entity History panel.
+     *
+     * `relPath` is repo-relative. Null parent (root commit, or file absent at the
+     * parent) → `created`. Result is immutable per (path, hash), so it's cached.
+     * Returns null only when the file isn't present at `hash`.
+     */
+    getCommitChange(relPath: string, hash: string): HistoryCommitChange | null;
+    /** Expose git service for deferred commit operations (SessionManager). */
     getGitService(): GitService | undefined;
+    /** Absolute repo path on disk. Used by callers that need to convert
+     *  an entity's absolute path to a repo-relative one (e.g. for `git log`). */
+    getRepoPath(): string;
+    /**
+     * Find an entity at a specific commit (existing or deleted) and
+     * return its repo-relative path + content. Public surface for the
+     * history tools — wraps the private `findEntityInCommit` walker.
+     * Returns null when no .md file at that commit matches the
+     * (entityType, entityId) pair.
+     */
+    getEntityAtCommit(entityType: EntityType, entityId: string, commitHash: string): {
+        path: string;
+        content: string;
+    } | null;
+    /** Workspace root passed in via GraphConfig. Used by the asset upload
+     *  service to anchor PDF text sidecars at workspace level (so all repos
+     *  share the same `assets-text/` tree, mirroring the shared
+     *  `.studiograph/assets/` directory the local backend uses). */
+    getWorkspaceRoot(): string | undefined;
+    /**
+     * Install structural-mutation callbacks. Called once after construction by
+     * the server bootstrap (or test setup) so the Yjs persistence layer can
+     * react to rename/delete/changeType without route-layer code calling
+     * persistence APIs directly.
+     */
+    setPersistenceCallbacks(callbacks: GraphPersistenceCallbacks | undefined): void;
+    /**
+     * Install the body-write coordinator. graph.update delegates the body-write
+     * critical section (lock, base-hash, atomic disk write, commit, broadcast,
+     * mdRevisionHash bookkeeping, assertWritable) to the coordinator. When
+     * unset (test fixtures without a Y.Doc layer), body writes fall back to a
+     * direct disk-write + commit path with no lock/broadcast — preserves the
+     * legacy "no callbacks" behavior some test setups rely on.
+     */
+    setBodyWriteCoordinator(coordinator: BodyWriteCoordinator | undefined): void;
     /**
      * Ensure repository exists
      */
     private ensureRepo;
     /**
-     * Get entity file path: {repo}/{plural-type}/{entityId}.md
+     * Compute the on-disk path for a new entity.
+     *
+     * - When `folderPath` is provided, the entry lives at {repo}/{folderPath}/{id}.md
+     *   regardless of type. This is the nested-folders layout.
+     * - Without `folderPath` (or empty string), the entry lands at the repo
+     *   root: {repo}/{id}.md. The historical {repo}/{plural-type}/{id}.md
+     *   fallback was confusing — entries hidden under a typed directory the
+     *   list view never showed at repo root, contradicting the agent tool
+     *   description that says "Omit to land at repo root."
+     *
+     * Note: this is for *new* paths only. Existing entries living under the
+     * legacy {plural-type}/ directories continue to be readable via
+     * findEntityFile() — only the create path moved.
      */
     private getEntityPath;
+    private fileIndex?;
+    /**
+     * Cache of the parsed `list()` view, keyed by `entityType ?? '*'`. Built
+     * lazily on first read; invalidated alongside `fileIndex` on every
+     * mutation. Without this, autosuggest walks the entire markdown tree
+     * and parses YAML frontmatter for every entry on every keystroke (5–7s
+     * on workspaces with a few thousand entries).
+     *
+     * Staleness contract: identical to `fileIndex` — single-process trust
+     * model. Git pulls and out-of-process file edits would equally miss
+     * the existing `fileIndex` cache; no regression there.
+     */
+    private listCache?;
+    /** Drop the cached file index so the next read rebuilds it. */
+    private invalidateIndex;
+    /**
+     * Walk every .md file under this repo, calling `visit` with the absolute
+     * path. Skips hidden directories (.git, .studiograph, etc.) and files that
+     * start with ".".
+     */
+    private walkMarkdownFiles;
+    /**
+     * Build (or fetch the cached) "type/id" → absolute path index.
+     * Type comes from frontmatter `entity_type`; if missing, falls back to the
+     * top-level plural-type directory name (legacy layout). Files without either
+     * (e.g. README.md) are skipped — they aren't entities.
+     */
+    private getFileIndex;
+    /**
+     * Infer entity type from a file's location for legacy layouts where the
+     * file sits directly inside a top-level plural-type directory
+     * ({repo}/meetings/foo.md). Returns undefined for any other layout.
+     */
+    private inferLegacyType;
+    /**
+     * Resolve an entity's absolute path by (type, id). Returns undefined if not
+     * found. Uses the file index — the index keys by `${entityType}/${entityId}`
+     * which is type-aware, unlike the on-disk filename. (We previously had a
+     * legacy {plural-type}/{id}.md fast path here; once the create path moved
+     * to flat repo-root layout, that fast path could return a different
+     * type's file at the same id.)
+     */
+    private findEntityFile;
     /**
      * Validate entity data against schema
      */
@@ -92,13 +376,48 @@ export declare class BaseGraphManager {
      */
     create(options: CreateEntityOptions): Promise<EntityFile>;
     /**
-     * Get an entity by type and ID
+     * Get an entity by type and ID. Searches nested folders if the entry isn't
+     * at the legacy {plural-type}/{id}.md path.
      */
     get(entityType: EntityType, entityId: string): EntityFile;
     /**
-     * Get an entity by ID only (type resolved from frontmatter)
+     * The live editor body for an entity when a seeded Y.Doc is open, else
+     * null. `get` reads disk, which lags the live Y.Doc by the autosave
+     * debounce + commit — so a user's freshly-placed image/asset embed exists
+     * in the editor before it reaches disk. Callers that must reflect what the
+     * user is actually looking at (the get_entity surfaces, the whole-body
+     * asset-drop guard) prefer this and fall back to disk on null.
+     *
+     * Returns null when no coordinator is wired (CLI / test fixtures) — those
+     * setups have no live editor layer, so disk IS the authoritative body.
+     */
+    getLiveBody(entityType: EntityType, entityId: string): string | null;
+    /**
+     * Get an entity by ID only (type resolved from the filesystem).
+     *
+     * Walks the file index to find any entry with this id, regardless of folder
+     * depth or type. Used by the agent's `get_entity` tool when the caller
+     * doesn't know the entity's type.
      */
     getById(entityId: string): EntityFile;
+    /**
+     * Merge a caller's `data` onto a base frontmatter, always stamping
+     * `updated_at` / `updated_by`, then validate. Even content-only edits
+     * (editor autosave, where `data` is undefined) re-stamp the audit fields —
+     * otherwise the trail freezes at whatever the last data-change user was,
+     * which for scaffolded files is "studiograph".
+     *
+     * `baseFrontmatter` is the frontmatter to merge onto. The body-write path
+     * passes the CURRENT on-disk frontmatter (read inside the per-doc lock) so
+     * a concurrent metadata-only edit isn't clobbered; the frontmatter-only
+     * path passes `existing.data` (synchronous, no lock window).
+     *
+     * Validation uses lenient mode + a Date-coercion fallback when no new data
+     * is supplied, since the existing entity may have been stored without all
+     * required fields, and gray-matter would otherwise serialize Date objects
+     * as full ISO timestamps.
+     */
+    private composeUpdatedFrontmatter;
     /**
      * Update an existing entity
      */
@@ -106,25 +425,193 @@ export declare class BaseGraphManager {
     /**
      * Delete an entity
      */
-    delete(entityType: EntityType, entityId: string, commitMessage?: string, user?: GitUser): Promise<void>;
+    /**
+     * Delete multiple entities in a single git transaction. Each entity's
+     * file is removed from disk; folder markers (.gitkeep) are added where
+     * the deletion left a folder empty. Then everything commits as one
+     * atomic operation.
+     *
+     * Compared to looping `delete()` per entity, this is a real performance
+     * primitive: one fork of git, one index update, one commit, one ref
+     * advance — instead of N. Bulk delete of a few hundred entities goes
+     * from minutes to seconds.
+     *
+     * Errors per entity (e.g. "not found") don't abort the batch — they're
+     * collected in `errors` and the rest still commit. Returns both the
+     * successfully-deleted set (for vector cleanup + WS broadcast) and the
+     * errors so the caller can surface partial failures.
+     */
+    bulkDelete(specs: Array<{
+        entityType: EntityType;
+        entityId: string;
+    }>, options?: {
+        commitMessage?: string;
+        user?: GitUser;
+    }): Promise<{
+        deleted: Array<{
+            entityType: EntityType;
+            entityId: string;
+            path: string;
+            title?: string;
+        }>;
+        errors: Array<{
+            entityType: EntityType;
+            entityId: string;
+            error: string;
+        }>;
+    }>;
+    /**
+     * Commit a set of already-on-disk file changes as a single git
+     * operation. Used by callers (e.g. the import route) that perform many
+     * `skipCommit: true` writes and want one transaction at the end instead
+     * of per-file commits.
+     *
+     * `entries` describes what each file represents so the transaction can
+     * be staged correctly. No-op when nothing is staged or git isn't
+     * available.
+     */
+    commitPending(entries: Array<{
+        operation: 'create' | 'update' | 'delete';
+        entityType: EntityType;
+        entityId: string;
+        filePath: string;
+    }>, options: {
+        commitMessage: string;
+        user?: GitUser;
+        extraPaths?: string[];
+    }): Promise<{
+        committed: boolean;
+    }>;
+    delete(entityType: EntityType, entityId: string, commitMessage?: string, user?: GitUser, opts?: {
+        keepAssets?: boolean;
+    }): Promise<void>;
     /**
      * Rename an entity (change its ID). Preserves all data, content, and source_ref.
      * Uses git mv for clean history. Updates entity_id in frontmatter.
      */
     rename(entityType: EntityType, oldId: string, newId: string, commitMessage?: string, user?: GitUser): Promise<EntityFile>;
     /**
-     * Change an entity's type. Moves the file from oldType/ to newType/ directory.
-     * Preserves all data and content. Updates entity_type in frontmatter.
+     * Change an entity's type. Updates frontmatter only — the file stays in
+     * its current folder. In the type-agnostic folder model, type is a
+     * frontmatter property independent of location. (Legacy behavior moved
+     * the file between {plural-type}/ dirs; that's no longer correct because
+     * those dirs are now ordinary user-visible folders, not type markers.)
+     *
+     * If the user wants the file to also move (e.g. out of a "meetings/"
+     * folder when changed to a note), they invoke move() separately.
      */
     changeType(entityId: string, fromType: EntityType, toType: EntityType, commitMessage?: string, user?: GitUser): Promise<EntityFile>;
     /**
-     * List entities of a given type
+     * Move an entry to a different folder within the same repo. The filename
+     * (and therefore the entity id) and type are unchanged. Auto-creates parent
+     * folders. Refuses if the target path already has an entry with this id —
+     * pass `overwrite: true` to replace it, but only when the occupant is
+     * itself a parseable entity (never silently clobber arbitrary files like
+     * README.md or .gitkeep).
+     */
+    move(entityType: EntityType, entityId: string, targetFolderPath: string, commitMessage?: string, user?: GitUser, overwrite?: boolean): Promise<EntityFile>;
+    /**
+     * Restore an entity to its content at a specific commit. Single-entity
+     * scope only — multi-entity rollback (e.g. "undo this commit's effects
+     * across all touched files") is a separate, more cautious flow that
+     * isn't built yet.
+     *
+     * Two paths through the method:
+     *   - **Overwrite**: the entity exists today at path `P`. Read content
+     *     from `git show <hash>:<P>` and write it back to `P`.
+     *   - **Recreate**: the entity is gone today. Walk the historical
+     *     commit's tree to find the .md file whose basename matches
+     *     `entityId` AND whose frontmatter `entity_type` matches
+     *     `entityType`. That path is the restore target. The walk only
+     *     fires when the entity is truly absent — overwrites stay cheap.
+     *
+     * Throws a `PathConflictError` if the recreate target path is now
+     * occupied by a DIFFERENT entity (different type+id) — recreating
+     * over it would silently overwrite unrelated work. Caller surfaces
+     * the conflict to the user; resolution is "move or delete the
+     * occupant first."
+     */
+    restoreFile(entityType: EntityType, entityId: string, commitHash: string, user?: GitUser): Promise<{
+        action: 'recreate' | 'overwrite';
+        path: string;
+    }>;
+    /**
+     * Walk a commit's tree looking for a .md file whose basename matches
+     * `entityId` AND whose frontmatter `entity_type` matches `entityType`.
+     * Returns repo-relative path + content when found, otherwise null.
+     * Used by `restoreFile` for the recreate-from-deletion case.
+     */
+    private findEntityInCommit;
+    /**
+     * Identify the entity (if any) currently occupying `absPath`. Returns
+     * null when the path holds something that isn't an entity (README, etc).
+     * Mirrors the inference rules used in `getFileIndex`.
+     */
+    private identifyEntityAtPath;
+    /**
+     * Enumerate the distinct entity types present in this repo. Used by
+     * /api/repos to let the sidebar render the Views list without a full
+     * entity fetch per folder.
+     *
+     * Derived from the file index (which reads frontmatter), so it works for
+     * entries in any folder — not just the legacy {plural-type}/ dirs.
+     */
+    listEntityTypes(): string[];
+    /**
+     * Folder lifecycle: a directory is treated as a first-class persistent
+     * object. It exists from the moment it's created (createFolder, the destination
+     * of a moved entry, etc.) until it's explicitly removed via a folder-level
+     * operation (deleteFolder, renameFolder, moveFolderToRepo). Entry-level
+     * operations (create, delete, move, transfer) never decide whether a folder
+     * lives or dies.
+     *
+     * `listFolders()` requires either a .md child or a .gitkeep marker for a
+     * directory to surface in the API, so the two helpers below are the single
+     * place that adds and removes the marker:
+     *
+     *  - `ensureFolderMarker` — call after an op that may have left `dir`
+     *    without .md children. Writes `.gitkeep` and returns its path so the
+     *    caller can stage it in the same commit.
+     *  - `removeFolderMarker` — call after an op that placed an .md into `dir`.
+     *    Drops a now-redundant `.gitkeep` so the repo stays tidy.
+     *
+     * Both no-op for the repo root (always implicit) and for paths that don't
+     * exist. Both return `null` when nothing changed.
+     */
+    private ensureFolderMarker;
+    private removeFolderMarker;
+    /**
+     * Walk up from `dir`, removing each directory that became empty after a
+     * folder-level removal (deleteFolder, renameFolder, moveFolderToRepo).
+     * Stops at the repo root. Silently no-ops if a directory is missing,
+     * non-empty, or can't be removed.
+     *
+     * NOT called by entry-level operations (create/delete/move/transfer) —
+     * they preserve folder structure regardless of whether they emptied a
+     * directory. Use `ensureFolderMarker` instead for those paths.
+     */
+    private pruneEmptyAncestors;
+    /**
+     * List entities of a given type (or all types if not specified).
+     *
+     * Walks the entire repo tree so entries in nested folders are discovered.
+     * The type filter is applied against frontmatter `entity_type`; legacy
+     * entries without explicit frontmatter type fall back to the depth-1
+     * plural-type directory name (so `meetings/foo.md` still resolves as a
+     * meeting). Files with no inferable type (README.md, CONTRIBUTING.md, etc.)
+     * are skipped.
      */
     list(entityType?: EntityType, limit?: number): EntityFile[];
     /**
      * Search entities
      */
     search(options: SearchOptions): EntityFile[];
+    /**
+     * Resolve a markdown file (anywhere under the repo) to its (type, id),
+     * tolerating both legacy {plural-type}/{id}.md and nested-folder layouts.
+     * Returns undefined for files without a recognizable entity type.
+     */
+    private resolveFileToEntity;
     /**
      * Get entities related to a given entity (via wikilinks)
      */
@@ -146,14 +633,219 @@ export declare class BaseGraphManager {
     refactorWikilink(oldId: string, newId: string, commitMessage?: string): Promise<{
         updated: number;
     }>;
+    /**
+     * List every non-empty folder in this repo, plus folders explicitly kept
+     * via .gitkeep. Returns repo-relative POSIX paths, sorted, deduplicated.
+     * The repo root ("") is intentionally omitted — it's implicit.
+     */
+    listFolders(): FolderEntry[];
+    /**
+     * Read the display_name override for a single folder, or null if no sidecar
+     * exists / is unreadable. Used by mutation paths that need the current
+     * override before deciding whether to rewrite it.
+     */
+    readFolderDisplayName(folderPath: string): string | null;
+    /**
+     * Write or remove the per-folder display_name sidecar. Pass `null` /
+     * empty-string to remove (returns to slug fallback). Returns the absolute
+     * path of the sidecar (for git staging) when one was written or removed,
+     * or null when no change was needed (idempotent).
+     *
+     * Caller is responsible for committing — the helper only touches the
+     * filesystem. Folder must already exist; this never creates one.
+     */
+    writeFolderDisplayName(folderPath: string, displayName: string | null): string | null;
+    /**
+     * Bulk-write display_name sidecars for many folders at once. Used by the
+     * import path to record original-casing overrides for every nested
+     * directory it slugified. First-writer-wins: existing sidecars are NOT
+     * overwritten, so a second import doesn't clobber a user's manual rename.
+     *
+     * Returns the list of sidecar paths actually written (for git staging).
+     * Skipped paths (folder missing, empty display, display_name override
+     * already set) are quietly omitted.
+     */
+    recordFolderDisplays(entries: Array<{
+        path: string;
+        display_name: string;
+    }>): string[];
+    /**
+     * Create a folder at the given path (mkdir -p semantics) and drop a
+     * .gitkeep so git tracks it even when empty. Validates the path. No-op if
+     * the folder already exists; .gitkeep is added if missing.
+     */
+    createFolder(folderPath: string, commitMessage?: string, user?: GitUser, options?: {
+        displayName?: string;
+    }): Promise<void>;
+    /**
+     * Rename / move a folder within the repo. Moves the entire subtree
+     * atomically via filesystem rename. Refuses if the target path is already
+     * occupied.
+     */
+    renameFolder(fromPath: string, toPath: string, commitMessage?: string, user?: GitUser, options?: {
+        displayName?: string | null;
+    }): Promise<void>;
+    /**
+     * Move a folder (and its full subtree) into a different repo at `targetFolderPath`.
+     *
+     * The naive way to do this is to iterate the source's entries and call
+     * `transfer` per entry — that's what the web UI used to do, and it costs
+     * 2 git commits per entry (1600 commits for 800 files), each blocking the
+     * Node event loop via `execSync`. This method performs the move as a
+     * single FS-level rename + one commit per repo, regardless of how many
+     * files are inside.
+     *
+     * Returns the count of entries + subfolders moved so the caller can
+     * surface progress.
+     */
+    moveFolderToRepo(sourceFolderPath: string, target: BaseGraphManager, targetFolderPath: string, options?: {
+        commitMessage?: string;
+        user?: GitUser;
+    }): Promise<FolderDeleteResult>;
+    /**
+     * Move a batch of entries (potentially across many source folders) into a
+     * single target folder, optionally in a different repo. The web UI's
+     * multi-select bulk move used to call /move or /transfer per entry — that
+     * was 1-2 sync git commits per entry, blocking the event loop on each one.
+     * This collapses the operation to a single FS rename per file plus one
+     * commit on each repo touched.
+     */
+    moveEntitiesToRepo(entries: Array<{
+        entityType: EntityType;
+        entityId: string;
+    }>, target: BaseGraphManager, targetFolderPath: string, options?: {
+        commitMessage?: string;
+        user?: GitUser;
+    }): Promise<{
+        moved: number;
+    }>;
+    /**
+     * Delete a folder. Refuses non-empty folders unless `recursive: true`.
+     * Returns the count of entries + subfolders removed (for blast-radius UI).
+     */
+    deleteFolder(folderPath: string, options?: {
+        recursive?: boolean;
+        commitMessage?: string;
+        user?: GitUser;
+    }): Promise<FolderDeleteResult>;
+    /**
+     * Count the entries (.md files with entity_type) and subfolders inside an
+     * absolute directory, recursively. Used to surface blast radius in the
+     * delete-folder approval UI.
+     */
+    private countFolderContents;
+    /**
+     * Return the storage backend the graph is bound to, or `undefined` if
+     * no asset service is configured. Used by routes that need to branch
+     * between local-stream and R2-redirect behavior.
+     */
+    getAssetStorage(): 'local' | 'r2' | undefined;
+    /** The asset storage service (raw key copy/exists), if configured. Used by
+     *  the one-time key migration, which operates on raw `{...}/{file}` keys. */
+    getAssetService(): AssetService | undefined;
+    /**
+     * Download the bytes of an asset OWNED by `assetEntityId` in THIS repo.
+     * Used by the convert flow to turn a stored .docx/.xlsx into a derived
+     * note/dataset. Backend-agnostic (local reads disk, R2 GetObjects).
+     *
+     * SECURITY: the asset's `asset_url` frontmatter is attacker-influenceable
+     * (a folder member can create an `asset` entity whose url points at another
+     * folder's storage key). So ownership is NOT taken from the url — it's
+     * resolved through the authoritative asset index, scoped to
+     * `(this.repoName, 'asset', assetEntityId)`, exactly like the GET
+     * /api/assets serve route. The url is used only to disambiguate which of the
+     * entity's own files to fetch (by filename). Unindexed legacy assets fall
+     * back to the legacy `asset/{entityId}/{file}` key bound to this same entity
+     * id; anything else is refused.
+     */
+    downloadOwnedAsset(assetEntityId: string, assetUrl: string): Promise<Buffer>;
+    /** Pre-signed URL for an immutable-key asset ({assetId}/{filename}). */
+    getAssetSignedUrlByAssetId(assetId: string, filename: string, method?: 'GET' | 'HEAD', expiresIn?: number): Promise<string>;
+    /**
+     * Mint a short-lived pre-signed URL for an asset. Only supported by
+     * remote backends (R2); the local backend throws. `method` selects
+     * the verb the URL is signed against — HEAD callers need a HEAD URL.
+     */
+    getAssetSignedUrl(entityType: EntityType, entityId: string, filename: string, keyPrefix?: string, expiresIn?: number, method?: 'GET' | 'HEAD'): Promise<string>;
     /**
      * Upload asset for an entity
      */
-    uploadAsset(entityType: EntityType, entityId: string, filename: string, buffer: Buffer, keyPrefix?: string): Promise<AssetInfo>;
+    uploadAsset(entityType: EntityType, entityId: string, filename: string, buffer: Buffer, keyPrefix?: string, 
+    /** Auth user id of the uploader (web). Recorded in the asset index for
+     *  the "delete by uploader + workspace owner" rule. Omit for CLI/import/
+     *  agent uploads — stored as null (unknown → owner-only delete). */
+    opts?: {
+        uploaderUserId?: string | null;
+        /**
+         * Override the recorded owner. Default = the `(entityType, entityId)`
+         * passed above (the entity that holds the blob — e.g. an image embedded
+         * in a note). The asset-as-embed model (see `~/.claude/plans/asset-as-embed.md`)
+         * uploads FREE-STANDING assets owned by a folder or the workspace, so the
+         * blob survives deletion/move of any entity that merely embeds it. When
+         * `owner` is set, `(entityType, entityId)` are ignored for ownership.
+         */
+        owner?: {
+            type: string;
+            id: string;
+        };
+        /** Display name recorded in the index row. Defaults to the filename.
+         *  Matters for free-standing assets, where the row's name is the manager
+         *  label (no owning entity to borrow a name from). */
+        name?: string;
+    }): Promise<AssetUploadResult>;
+    /** Inject the workspace-global asset ownership index (WorkspaceManager). */
+    setAssetIndex(index: AssetIndexService | undefined): void;
+    /** The asset ownership index, if wired. */
+    getAssetIndex(): AssetIndexService | undefined;
+    /**
+     * Remove every immutable-keyed asset owned by (entityType, entityId): the
+     * blob + its index row. Used by delete/bulkDelete/deleteFolder. Blob errors
+     * are non-fatal (markdown is the system of record). No-op without an index.
+     * Owner-scoped, so it only touches THIS entity's assets — a blob another
+     * entity also embeds (copied URL) is not enumerated here.
+     */
+    private cleanupOwnedAssets;
+    /** Delete a single index-tracked asset by its immutable id: blob + index row.
+     *  The asset-manager delete path for free-standing (folder/workspace-owned)
+     *  assets, which have no owning entity to route an entity-coordinate delete
+     *  through. Blob errors are non-fatal (the index row is the manager's source
+     *  of truth, same as cleanupOwnedAssets). No-op without an index/service. */
+    deleteAssetById(assetId: string, filename: string): Promise<void>;
+    /** Re-point the owning coordinates of every asset owned by an entity, with
+     *  no blob movement (keys are immutable). Used by rename (ownerId),
+     *  changeType (ownerType), and cross-repo move/transfer (repo). No-op
+     *  without an index. */
+    private reassignOwnedAssets;
     /**
      * List assets for an entity
      */
     listAssets(entityType: EntityType, entityId: string, keyPrefix?: string): Promise<AssetInfo[]>;
+    /**
+     * List every asset in the backend in one round-trip, tagged with
+     * (entityType, entityId) origin. Workspace-wide since the asset backend
+     * is shared across repos — callers filter by repo via {@link listEntityIds}.
+     */
+    listAllAssets(): Promise<AssetRecord[]>;
+    /**
+     * Enumerate (type, id) pairs in this repo. Used by endpoints (like
+     * /api/repos/:repo/assets) that need to answer "does entity X belong to
+     * this repo?".
+     *
+     * Backed by the file index, which reads frontmatter — so entries in
+     * nested folders are included alongside legacy {plural-type}/ entries.
+     */
+    listEntityIds(): Array<{
+        entityType: EntityType;
+        id: string;
+    }>;
+    /**
+     * Resolve the absolute on-disk markdown path for an entity. Goes through
+     * the file index so it works for both the flat repo-root layout and
+     * arbitrary nested folders. Use this anywhere callers need a path —
+     * never reconstruct one from `${plural-type}/${id}.md`, which assumes
+     * the legacy typed-folder layout and silently misses everything else.
+     */
+    getEntityFilePath(entityType: EntityType, entityId: string): string | undefined;
     /**
      * Delete an asset
      */
@@ -163,13 +855,38 @@ export declare class BaseGraphManager {
      */
     deleteAllAssets(entityType: EntityType, entityId: string, keyPrefix?: string): Promise<number>;
     /**
-     * Get dataset rows, optionally filtered
+     * Resolve the authoritative CSV body for a dataset: the live editor body
+     * when one exists (the grid may be ahead of disk), else the on-disk body.
+     */
+    private datasetBody;
+    /**
+     * Get dataset rows, optionally filtered. Columns come from the CSV header.
      */
     getDatasetRows(entityId: string, filter?: DatasetFilter): DatasetRow[];
     /**
-     * Append rows to a dataset entity
+     * Column names for a dataset, read from the CSV header. Independent of the
+     * rows so callers get the real columns even for a header-only dataset or a
+     * zero-match filter (where deriving columns from result rows would be empty).
+     */
+    getDatasetColumns(entityId: string): string[];
+    /**
+     * Append rows to a dataset entity.
+     *
+     * The existing CSV body is preserved verbatim and the new rows are appended
+     * after it — we do NOT re-parse and re-stringify existing rows. That keeps
+     * datasets with duplicate column headers from collapsing (csv-parse's
+     * object mode keeps only the last same-named column) and avoids reformatting
+     * unrelated cells. New rows are mapped to the existing header columns; keys
+     * not in the header are dropped (query the columns first). When the body has
+     * no header yet, the columns are taken from the new rows.
+     *
+     * The write routes through `update()` so it shares the BodyWriteCoordinator
+     * contract (per-doc lock, base-hash precondition, applyAgentContent, commit)
+     * instead of writing to disk directly — same guarantees the agent's markdown
+     * writes get. `baseRevision` makes a concurrent change since our read fail
+     * loudly rather than silently back-stomp.
      */
-    appendDatasetRows(entityId: string, newRows: DatasetRow[], commitMessage?: string): Promise<EntityFile>;
+    appendDatasetRows(entityId: string, newRows: Array<Record<string, unknown>>, commitMessage?: string): Promise<EntityFile>;
     /**
      * Get repository status
      */