mrplex 0.0.1

package/dist/sync/reconcile.js

@@ -0,0 +1,252 @@
+/**
+ * Startup reconciliation (sync/history plan §4.9) — the entirety of
+ * `mrplex sync --once`. No watcher, no remote deletes (by construction, §4.6).
+ *
+ * The pass walks the remote live set (history.index through a safe head R) and
+ * the local files, then resolves each path/identity against the §4.9 table.
+ * Every verdict is deterministic and non-destructive: local edits are pushed,
+ * clean local copies adopt remote provenance in place, and true conflicts park
+ * the remote current as an ignored sibling rather than clobbering local bytes.
+ *
+ * This module is transport-agnostic: it drives a `KernelClient` and a small
+ * `FileStore` seam (real fs in `fs-store.ts`, in-memory in tests), so the whole
+ * §4.9 table is testable against a local kernel without touching disk.
+ */
+import { withVersionSuffix } from "../kernel/deletion.js";
+import { KernelError } from "../kernel/errors.js";
+import { extractSystemProperties, split } from "../markdown/frontmatter.js";
+import { isDirty, isIgnored, readFileIntrinsics, renderIgnoredSibling, renderMaterialized, } from "./intrinsics.js";
+/**
+ * Run the full §4.9 reconciliation once. Returns the safe head R (the cursor to
+ * persist) and the list of actions taken (or planned, under dryRun).
+ */
+export async function reconcileOnce(client, store, scope, opts) {
+    const actions = [];
+    const dryRun = opts.dryRun ?? false;
+    const log = opts.log ?? (() => { });
+    // 1. Enumerate the remote live set through a safe head R (§3.4). Keyset-page.
+    const remoteByPath = new Map();
+    let through;
+    let after;
+    for (;;) {
+        const page = await client.history.index({
+            repo: opts.repo,
+            through_version: through,
+            after_version: after,
+        });
+        through = page.through_version;
+        for (const item of page.items) {
+            if (scope.matches(item.path))
+                remoteByPath.set(item.path, item);
+        }
+        if (page.next_after_version === undefined)
+            break;
+        after = page.next_after_version;
+    }
+    const R = through ?? "";
+    // Index remote items by embedded version id too, for move detection (§4.7).
+    const remoteByVersion = new Map();
+    for (const item of remoteByPath.values())
+        remoteByVersion.set(item.version_id, item);
+    // 2. Walk local files (in scope; $sync: ignore excluded from the walk, §4.9).
+    const localPaths = (await store.list()).filter((p) => scope.matches(p));
+    const seenRemote = new Set();
+    for (const path of localPaths) {
+        const text = await store.read(path);
+        if (text === null)
+            continue; // vanished between list and read — skip
+        const intr = readFileIntrinsics(text);
+        if (isIgnored(intr)) {
+            actions.push({ path, verdict: "ignored" });
+            continue;
+        }
+        const remote = remoteByPath.get(path);
+        if (remote)
+            seenRemote.add(path);
+        const action = await resolveLocalPath(client, store, opts, dryRun, {
+            path,
+            intr,
+            remote,
+            remoteByVersion,
+        });
+        actions.push(action);
+    }
+    // 3. Remote docs with no local file → materialize (§4.9 row 9; the offline
+    //    concession restoring deletes). Never a remote delete.
+    for (const [path, item] of remoteByPath) {
+        if (seenRemote.has(path))
+            continue;
+        if (!dryRun) {
+            const v = await client.docs.get_version(opts.repo, item.version_id);
+            await store.write(path, renderMaterialized(v));
+        }
+        actions.push({ path, verdict: "materialize", detail: "remote doc absent locally" });
+    }
+    for (const a of actions) {
+        if (a.verdict !== "clean" && a.verdict !== "skip") {
+            log(`${a.verdict}\t${a.path}${a.detail ? `\t(${a.detail})` : ""}`);
+        }
+    }
+    return { through_version: R, actions };
+}
+/** Resolve one local file against its remote counterpart (the §4.9 table). */
+async function resolveLocalPath(client, store, opts, dryRun, ctx) {
+    const { path, intr, remote } = ctx;
+    const dirty = isDirty(intr);
+    if (remote) {
+        // A document lives at this path remotely.
+        if (intr.computed_hash === remote.content_hash) {
+            // Local user-bytes already equal the remote version — a clean equivalence
+            // even if the file has no embedded provenance (row 2) or stale intrinsics.
+            // Path equality alone never suffices; only this hash match licenses
+            // stamping the remote $version. Metadata-only, no server write.
+            if (intr.version === remote.version_id && intr.content_hash === remote.content_hash) {
+                return { path, verdict: "clean" };
+            }
+            if (!dryRun)
+                await materializeInPlace(client, store, opts.repo, path, remote.version_id);
+            return { path, verdict: "adopt", detail: "content matches remote; provenance repaired" };
+        }
+        if (!intr.version) {
+            // No embedded version and bytes differ from remote → occupied-path
+            // conflict (row 6). Never stamp divergent local bytes with remote id.
+            if (!dryRun)
+                await parkConflict(client, store, opts.repo, path, remote.version_id);
+            return { path, verdict: "conflict", detail: "occupied path, no local provenance" };
+        }
+        if (intr.version === remote.version_id) {
+            // Embedded version is the remote current.
+            if (!dirty)
+                return { path, verdict: "clean" };
+            // Local edit on top of the current → push (row 4).
+            if (!dryRun)
+                await pushEdit(client, store, opts.repo, path, intr.version);
+            return { path, verdict: "push", detail: "local edit on current" };
+        }
+        // Embedded version differs from remote current.
+        if (!dirty) {
+            // Local unedited but stale → fast-forward to remote current (row 3).
+            if (!dryRun)
+                await materializeVersion(client, store, opts.repo, path, remote.version_id);
+            return { path, verdict: "materialize", detail: "fast-forward to remote current" };
+        }
+        // Local edited AND remote advanced → conflict (row 5).
+        if (!dryRun)
+            await parkConflict(client, store, opts.repo, path, remote.version_id);
+        return { path, verdict: "conflict", detail: "local edit vs advanced remote" };
+    }
+    // No remote doc at this path.
+    const embeddedVersion = intr.version;
+    const known = embeddedVersion ? ctx.remoteByVersion.get(embeddedVersion) : undefined;
+    if (known && embeddedVersion) {
+        // Embedded version is known at a DIFFERENT remote path → a move (row 8).
+        // The clean/dirty + conflict subtleties of live moves belong to the daemon;
+        // for --once we push the move (put with the new path) when the local file
+        // carries the ancestry. A stale_prev downgrades to a conflict.
+        if (!dryRun) {
+            try {
+                await pushMove(client, store, opts.repo, path, embeddedVersion);
+            }
+            catch (err) {
+                if (err instanceof KernelError && err.code === "stale_prev") {
+                    await parkConflictForCurrent(client, store, opts.repo, path, embeddedVersion);
+                    return { path, verdict: "conflict", detail: "move raced remote change" };
+                }
+                throw err;
+            }
+        }
+        return { path, verdict: "push", detail: `move from ${known.path}` };
+    }
+    if (!intr.version) {
+        // No provenance, path absent remotely → a genuine local creation (row 7).
+        if (!dryRun)
+            await pushCreate(client, store, opts.repo, path);
+        return { path, verdict: "push", detail: "local creation" };
+    }
+    // Embedded version exists but the document is no longer live at this path and
+    // isn't known elsewhere → it was remotely deleted. Clean removes locally;
+    // dirty resurrects (push as create). Never discard dirty bytes (§4.9 edge).
+    if (!dirty) {
+        if (!dryRun)
+            await store.remove(path);
+        return { path, verdict: "delete-local", detail: "remote-deleted, local clean" };
+    }
+    if (!dryRun)
+        await pushCreate(client, store, opts.repo, path);
+    return { path, verdict: "resurrect", detail: "remote-deleted, local dirty" };
+}
+// --- effecting helpers -------------------------------------------------------
+async function readUserContent(store, path) {
+    const text = (await store.read(path)) ?? "";
+    return stripToUserContent(text);
+}
+/** Split a file into stored-shape fields, dropping all `$*` intrinsic lines. */
+function stripToUserContent(text) {
+    const lf = text.replace(/\r\n/g, "\n");
+    // Reuse the same split/strip path the hash uses so bytes are canonical.
+    const { frontmatter_raw, body } = split(lf);
+    return { frontmatter_raw: extractSystemProperties(frontmatter_raw).raw, body };
+}
+async function materializeVersion(client, store, repo, path, versionId) {
+    const v = await client.docs.get_version(repo, versionId);
+    await store.write(path, renderMaterialized(v));
+}
+/** Repair a clean local file's embedded provenance to the given version. */
+async function materializeInPlace(client, store, repo, path, versionId) {
+    // The content already equals the version; re-render from the authoritative
+    // remote version so intrinsics are exact. Keep mtime so a metadata-only
+    // stamp cannot win an Obsidian/iCloud race against unsynced typing.
+    const v = await client.docs.get_version(repo, versionId);
+    await store.write(path, renderMaterialized(v), { preserveMtime: true });
+}
+async function pushEdit(client, store, repo, path, prevVersionId) {
+    const { frontmatter_raw, body } = await readUserContent(store, path);
+    const v = await client.docs.put(repo, prevVersionId, path, { frontmatter_raw, body });
+    await store.write(path, renderMaterialized(v), { preserveMtime: true });
+}
+async function pushMove(client, store, repo, path, prevVersionId) {
+    const { frontmatter_raw, body } = await readUserContent(store, path);
+    // A put whose path differs from prev's path is a move preserving identity.
+    const v = await client.docs.put(repo, prevVersionId, path, { frontmatter_raw, body });
+    await store.write(path, renderMaterialized(v), { preserveMtime: true });
+}
+async function pushCreate(client, store, repo, path) {
+    const { frontmatter_raw, body } = await readUserContent(store, path);
+    try {
+        const v = await client.docs.create(repo, path, { frontmatter_raw, body });
+        await store.write(path, renderMaterialized(v), { preserveMtime: true });
+    }
+    catch (err) {
+        if (err instanceof KernelError && err.code === "create_conflict") {
+            // A doc appeared at this path since the index scan; treat the occupied
+            // path as a conflict rather than clobbering it.
+            const current = err.data.current_version_id;
+            if (current)
+                await parkConflict(client, store, repo, path, current);
+            return;
+        }
+        throw err;
+    }
+}
+/**
+ * Park a conflict (§4.8): keep the local file's bytes and path untouched;
+ * materialize the remote current beside it as `<name>-<version_id>.md` with
+ * `$sync: ignore`. Collision-safe (version ids are unique), so replay never
+ * sprays duplicates.
+ */
+async function parkConflict(client, store, repo, path, remoteVersionId) {
+    const v = await client.docs.get_version(repo, remoteVersionId);
+    const siblingPath = withVersionSuffix(path, remoteVersionId);
+    await store.write(siblingPath, renderIgnoredSibling(v));
+}
+/** Conflict park keyed off the doc's *current* remote version (move race). */
+async function parkConflictForCurrent(client, store, repo, path, embeddedVersionId) {
+    // Resolve the document's current version from the embedded (now-superseded)
+    // one, then park it. get_version gives us the doc; docs.get by its path finds
+    // the live current.
+    const superseded = await client.docs.get_version(repo, embeddedVersionId);
+    const current = await client.docs.get(repo, superseded.path);
+    const siblingPath = withVersionSuffix(path, current.version_id);
+    await store.write(siblingPath, renderIgnoredSibling(current));
+}
+//# sourceMappingURL=reconcile.js.map

package/dist/sync/reconcile.js.map

@@ -0,0 +1 @@
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package/dist/sync/run.d.ts

@@ -0,0 +1,27 @@
+/**
+ * `mrplex sync --once` orchestration (sync/history plan §4.9). Runs the full
+ * startup reconciliation, then applies the feed from R and advances the cursor.
+ * The daemon (M8) layers a watcher + poll loop over these same pieces.
+ */
+import type { KernelClient } from "../client/kernel-client.js";
+import { type ReconcileReport } from "./reconcile.js";
+export type SyncOnceOptions = {
+    root: string;
+    repo: string;
+    server?: string;
+    database?: string;
+    include?: string[];
+    exclude?: string[];
+    dryRun?: boolean;
+    log?: (msg: string) => void;
+};
+export type SyncOnceReport = ReconcileReport & {
+    feed_applied: number;
+};
+/**
+ * The full once-pass: index reconciliation through R, then drain
+ * history.since(R) to catch anything that advanced during the scan, then
+ * persist the cursor. `--once` always performs the full reconciliation (§4.9),
+ * so it also restores offline deletes and propagates offline moves.
+ */
+export declare function syncOnce(client: KernelClient, opts: SyncOnceOptions): Promise<SyncOnceReport>;

package/dist/sync/run.js

@@ -0,0 +1,46 @@
+/**
+ * `mrplex sync --once` orchestration (sync/history plan §4.9). Runs the full
+ * startup reconciliation, then applies the feed from R and advances the cursor.
+ * The daemon (M8) layers a watcher + poll loop over these same pieces.
+ */
+import { readCursor, sourceFields, writeCursor } from "./cursor.js";
+import { applyFeed } from "./feed.js";
+import { createFsStore } from "./fs-store.js";
+import { makeScopeFilter } from "./paths.js";
+import { reconcileOnce } from "./reconcile.js";
+/**
+ * The full once-pass: index reconciliation through R, then drain
+ * history.since(R) to catch anything that advanced during the scan, then
+ * persist the cursor. `--once` always performs the full reconciliation (§4.9),
+ * so it also restores offline deletes and propagates offline moves.
+ */
+export async function syncOnce(client, opts) {
+    const store = createFsStore(opts.root);
+    const scope = makeScopeFilter({ include: opts.include, exclude: opts.exclude });
+    const report = await reconcileOnce(client, store, scope, {
+        repo: opts.repo,
+        dryRun: opts.dryRun,
+        log: opts.log,
+    });
+    if (opts.dryRun)
+        return { ...report, feed_applied: 0 };
+    // Apply the feed from R forward: documents that advanced mid-scan land here
+    // exactly once (§3.4 handoff invariant). The feed returns its final cursor.
+    const { cursor, applied } = await applyFeed(client, store, scope, {
+        repo: opts.repo,
+        since: report.through_version,
+        log: opts.log,
+    });
+    // Persist the cursor only after all filesystem effects complete (§4.3).
+    // Record the source as exactly one of server/database, falling back to
+    // whichever the existing marker carried so an incidental re-run doesn't drop
+    // it. server/database are mutually exclusive, so a set server wins outright.
+    const existing = await readCursor(opts.root);
+    await writeCursor(opts.root, {
+        ...sourceFields(opts.server, opts.database, existing),
+        repo: opts.repo,
+        last_synced_version_id: cursor,
+    });
+    return { ...report, feed_applied: applied };
+}
+//# sourceMappingURL=run.js.map

package/dist/sync/run.js.map

@@ -0,0 +1 @@
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package/dist/version.d.ts

@@ -0,0 +1,2 @@
+/** Package version — single source for CLI and MCP server metadata. */
+export declare const VERSION: string;

package/dist/version.js

@@ -0,0 +1,5 @@
+import { createRequire } from "node:module";
+const require = createRequire(import.meta.url);
+/** Package version — single source for CLI and MCP server metadata. */
+export const VERSION = require("../package.json").version;
+//# sourceMappingURL=version.js.map

package/dist/version.js.map

@@ -0,0 +1 @@
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package/package.json

@@ -0,0 +1,80 @@
+{
+  "name": "mrplex",
+  "version": "0.0.1",
+  "description": "Markdown Repos, plexed. Turn Markdown folders into queryable, versioned, graph-aware knowledge stores.",
+  "type": "module",
+  "license": "MIT",
+  "author": "Brendan Baldwin <brendan@usergenic.com>",
+  "repository": {
+    "type": "git",
+    "url": "git+https://github.com/usergenic/mrplex.git"
+  },
+  "homepage": "https://github.com/usergenic/mrplex#readme",
+  "bugs": {
+    "url": "https://github.com/usergenic/mrplex/issues"
+  },
+  "keywords": [
+    "markdown",
+    "knowledge-base",
+    "notes",
+    "versioning",
+    "graph",
+    "backlinks",
+    "wikilinks",
+    "cel",
+    "mcp",
+    "semantic-search"
+  ],
+  "publishConfig": {
+    "access": "public"
+  },
+  "bin": {
+    "mrplex": "./dist/cli/main.js"
+  },
+  "files": ["dist/"],
+  "scripts": {
+    "prepack": "npm run build",
+    "build": "tsc -p tsconfig.build.json && node scripts/copy-assets.mjs && node scripts/set-script-permissions.mjs",
+    "typecheck": "tsc --noEmit",
+    "lint": "biome check .",
+    "lint:fix": "biome check --write .",
+    "format": "biome format --write .",
+    "test": "vitest run",
+    "test:watch": "vitest",
+    "test:integration": "vitest run --config vitest.integration.config.ts",
+    "test:all": "vitest run && vitest run --config vitest.integration.config.ts",
+    "cli": "tsx src/cli/main.ts",
+    "seed": "tsx scripts/seed.ts",
+    "pg:up": "docker compose --profile postgres up -d",
+    "pg:down": "docker compose --profile postgres down",
+    "pg:reset": "docker compose --profile postgres down -v && docker compose --profile postgres up -d",
+    "pg:logs": "docker compose --profile postgres logs -f postgres"
+  },
+  "engines": {
+    "node": ">=20.11.0"
+  },
+  "dependencies": {
+    "@bufbuild/cel": "^0.6.0",
+    "@bufbuild/re2": "^0.6.0",
+    "@modelcontextprotocol/sdk": "^1.30.0",
+    "better-sqlite3": "^11.5.0",
+    "chokidar": "^5.0.0",
+    "commander": "^12.1.0",
+    "diff": "^9.0.0",
+    "jose": "^6.2.9",
+    "micromark": "^4.0.2",
+    "pg": "^8.23.0",
+    "sqlite-vec": "^0.1.9",
+    "yaml": "^2.6.0"
+  },
+  "devDependencies": {
+    "@biomejs/biome": "^1.9.4",
+    "@types/better-sqlite3": "^7.6.11",
+    "@types/diff": "^7.0.2",
+    "@types/node": "^22.9.0",
+    "@types/pg": "^8.21.0",
+    "tsx": "^4.19.2",
+    "typescript": "^5.6.3",
+    "vitest": "^4.1.10"
+  }
+}