fix(server): heal 0000-baseline schema drift after baselining existing installs

baselineExistingInstall marks 0000_initial as applied when it detects
pre-existing tables, on the assumption the install's schema matches the
0000 baseline. That assumption is false for dev DBs created under the
pre-drizzle manual migrate.ts system that skipped or never ran some of
its idempotent ALTER TABLE steps — for example the b9e4c65 migration
that added federation_peers.remote_max_upload_size. On such DBs, 0000
is marked done without the column actually existing, and a later
migration that recreates the table (0004_cooing_black_knight)
subsequently crashes with "no such column: remote_max_upload_size"
while building its __new_federation_peers SELECT.

Adds healInitialSchemaDrift(): walks every table in 0000_snapshot.json,
and for each table that already exists, ADDs any columns the snapshot
declares but the physical table is missing. Runs immediately after
baselining, before drizzle's migrate() — so later migrations find the
schema they expect. Columns that SQLite's ALTER TABLE ADD COLUMN can't
safely express (PRIMARY KEY; NOT NULL without a default) are skipped
with a warning rather than corrupting data.

Idempotent: on fresh installs and correctly-migrated DBs every column
is already present, so the loop is a no-op. Production Pi+VM instances
are unaffected.

Verification: local dev DB that previously crashed on 0004 now boots
cleanly — federation_peers gained remote_max_upload_size, nonce_supported,
pending_hmac_secret, secret_rotation_at, secret_rotated_at, and
auto_rotate_interval_days; __drizzle_migrations advanced from 4 to 5
entries; server binds :3005. 110/110 server tests + 131/131 web tests
still pass.

Not covered: a deeper drift on federation_outbox /
federation_mutation_log where the physical tables retain pre-rename
column names (message_id / dm_channel_id) instead of the current
entity_id / context_id. Heal skips those (NOT NULL without default)
and the outbox worker emits SQLITE_ERROR ticks post-boot. Both tables
are empty on affected dev DBs, but a clean fix requires DROP +
RECREATE with index reinstatement which is out of #29's stated scope
("column existing"). Flagged for a follow-up.

Closes backlog #29.

packages/server/src/db/index.ts

@@ -3,7 +3,7 @@ import { drizzle } from 'drizzle-orm/better-sqlite3';
 import { migrate } from 'drizzle-orm/better-sqlite3/migrator';
 import { config } from '../config.js';
 import * as schema from './schema.js';
-import { baselineExistingInstall, ensureDefaults } from './migrate.js';
+import { baselineExistingInstall, healInitialSchemaDrift, ensureDefaults } from './migrate.js';
 import { setWorkerId } from '../utils/snowflake.js';
 import { mkdirSync } from 'fs';
 import { dirname, resolve } from 'path';
@@ -29,6 +29,12 @@ export function initDatabase() {
   // CREATE TABLE on a database that already has tables.
   baselineExistingInstall(sqlite);
 
+  // Reconcile any columns present in the 0000 baseline but missing
+  // from the physical schema. Fixes drift between the pre-drizzle
+  // manual migration system and drizzle-kit's assumed baseline —
+  // a no-op on fresh installs and correctly-migrated DBs.
+  healInitialSchemaDrift(sqlite);
+
   // Apply any pending Drizzle migrations
   const migrationsFolder = resolve(__dirname, '../../drizzle');
   const db = drizzle(sqlite, { schema });

packages/server/src/db/migrate.ts

@@ -64,6 +64,82 @@ export function baselineExistingInstall(db: Database.Database): void {
   console.log(`[migrate] Baselined initial migration: ${initialEntry.tag} (hash: ${hash.slice(0, 12)}...)`);
 }
 
+/**
+ * Heal column drift between an existing install and the 0000_initial
+ * schema baseline.
+ *
+ * The baseline in `baselineExistingInstall` assumes that any existing
+ * install's schema already matches 0000_initial.sql. That assumption is
+ * usually fine for installs created through the old pre-drizzle manual
+ * migration system — but a DB can fall behind if it skipped one of those
+ * manual ALTERs (e.g. a dev-env that was paused before the
+ * `remote_max_upload_size` migration in 1e4e71a landed). On such DBs,
+ * baseline marks 0000 as applied without the columns actually being
+ * there, and a later migration that recreates the table (e.g.
+ * 0004_cooing_black_knight) crashes trying to SELECT them.
+ *
+ * Walks every table defined in 0000_snapshot.json; for each that already
+ * exists in the DB, ADDs any columns the snapshot declares but the table
+ * is missing. Idempotent: on a correctly-migrated DB every column is
+ * already present and the loop is a no-op. Columns that SQLite's
+ * ALTER TABLE ADD COLUMN cannot express (PRIMARY KEY; NOT NULL without a
+ * default) are skipped with a warning rather than corrupting data.
+ *
+ * Only reconciles against the 0000 baseline — later migrations add their
+ * own columns through normal migration SQL and are handled by
+ * Drizzle's migrator.
+ */
+export function healInitialSchemaDrift(db: Database.Database): void {
+  const migrationsFolder = path.resolve(__dirname, '../../drizzle');
+  const snapshotPath = path.join(migrationsFolder, 'meta', '0000_snapshot.json');
+  const snapshot = JSON.parse(fs.readFileSync(snapshotPath, 'utf-8')) as {
+    tables: Record<string, {
+      name: string;
+      columns: Record<string, {
+        name: string;
+        type: string;
+        primaryKey: boolean;
+        notNull: boolean;
+        autoincrement: boolean;
+        default?: string | number;
+      }>;
+    }>;
+  };
+
+  for (const table of Object.values(snapshot.tables)) {
+    const exists = db.prepare(
+      "SELECT name FROM sqlite_master WHERE type='table' AND name=?"
+    ).get(table.name);
+    if (!exists) continue;
+
+    const existingCols = new Set(
+      (db.prepare(`PRAGMA table_info("${table.name}")`).all() as { name: string }[])
+        .map(c => c.name)
+    );
+
+    for (const col of Object.values(table.columns)) {
+      if (existingCols.has(col.name)) continue;
+
+      if (col.primaryKey) {
+        console.warn(`[migrate] Skipping drift heal for ${table.name}.${col.name}: PRIMARY KEY cannot be added via ALTER TABLE`);
+        continue;
+      }
+      if (col.notNull && col.default === undefined) {
+        console.warn(`[migrate] Skipping drift heal for ${table.name}.${col.name}: NOT NULL with no default (would violate existing rows)`);
+        continue;
+      }
+
+      const parts = [`"${col.name}"`, col.type];
+      if (col.notNull) parts.push('NOT NULL');
+      if (col.default !== undefined) parts.push(`DEFAULT ${col.default}`);
+
+      const sql = `ALTER TABLE "${table.name}" ADD COLUMN ${parts.join(' ')}`;
+      console.log(`[migrate] Healing schema drift: ${sql}`);
+      db.exec(sql);
+    }
+  }
+}
+
 /**
  * Ensure data invariants after schema migration. Idempotent — safe to run
  * on every boot. Uses raw better-sqlite3 handle (not Drizzle ORM).