fix: add missing deleted_at columns to all plugin tables, fix system-settings response schema, fix transaction rollback in permissions

app/plugins/builtins/calendar/migrations/0001_initial.sql

@@ -46,7 +46,10 @@ CREATE TABLE IF NOT EXISTS calendar_entry_links (
     tenant_id UUID NOT NULL,
     entry_id UUID REFERENCES calendar_entries(id) ON DELETE CASCADE,
     entity_type VARCHAR(50) NOT NULL,
-    entity_id UUID NOT NULL
+    entity_id UUID NOT NULL,
+    deleted_at TIMESTAMPTZ,
+    created_at TIMESTAMPTZ DEFAULT NOW(),
+    updated_at TIMESTAMPTZ DEFAULT NOW()
 );
 CREATE INDEX IF NOT EXISTS idx_entry_links_entry ON calendar_entry_links(entry_id);
 
@@ -56,7 +59,10 @@ CREATE TABLE IF NOT EXISTS calendar_shares (
     calendar_id UUID REFERENCES calendars(id) ON DELETE CASCADE,
     user_id UUID,
     group_id UUID,
-    permission VARCHAR(10) NOT NULL
+    permission VARCHAR(10) NOT NULL,
+    deleted_at TIMESTAMPTZ,
+    created_at TIMESTAMPTZ DEFAULT NOW(),
+    updated_at TIMESTAMPTZ DEFAULT NOW()
 );
 CREATE INDEX IF NOT EXISTS idx_calendar_shares_cal ON calendar_shares(calendar_id);
 
@@ -74,7 +80,9 @@ CREATE TABLE IF NOT EXISTS subtasks (
     entry_id UUID REFERENCES calendar_entries(id) ON DELETE CASCADE,
     title VARCHAR(500) NOT NULL,
     completed BOOLEAN DEFAULT false,
-    created_at TIMESTAMPTZ DEFAULT NOW()
+    deleted_at TIMESTAMPTZ,
+    created_at TIMESTAMPTZ DEFAULT NOW(),
+    updated_at TIMESTAMPTZ DEFAULT NOW()
 );
 CREATE INDEX IF NOT EXISTS idx_subtasks_entry ON subtasks(entry_id);
 
@@ -82,7 +90,10 @@ CREATE TABLE IF NOT EXISTS resources (
     id UUID PRIMARY KEY DEFAULT gen_random_uuid(),
     tenant_id UUID NOT NULL,
     name VARCHAR(200) NOT NULL,
-    type VARCHAR(50) NOT NULL
+    type VARCHAR(50) NOT NULL,
+    deleted_at TIMESTAMPTZ,
+    created_at TIMESTAMPTZ DEFAULT NOW(),
+    updated_at TIMESTAMPTZ DEFAULT NOW()
 );
 CREATE INDEX IF NOT EXISTS idx_resources_tenant ON resources(tenant_id);
 
@@ -92,7 +103,10 @@ CREATE TABLE IF NOT EXISTS resource_bookings (
     resource_id UUID REFERENCES resources(id) ON DELETE CASCADE,
     entry_id UUID REFERENCES calendar_entries(id) ON DELETE CASCADE,
     start_at TIMESTAMPTZ NOT NULL,
-    end_at TIMESTAMPTZ NOT NULL
+    end_at TIMESTAMPTZ NOT NULL,
+    deleted_at TIMESTAMPTZ,
+    created_at TIMESTAMPTZ DEFAULT NOW(),
+    updated_at TIMESTAMPTZ DEFAULT NOW()
 );
 CREATE INDEX IF NOT EXISTS idx_bookings_resource ON resource_bookings(resource_id);
 CREATE INDEX IF NOT EXISTS idx_bookings_entry ON resource_bookings(entry_id);

app/plugins/builtins/calendar/migrations/0002_add_deleted_at.sql

@@ -0,0 +1,17 @@
+-- Fix: CalendarEntryLink, CalendarShare, Subtask, Resource, ResourceBooking inherit TenantMixin -> SoftDeleteMixin (deleted_at)
+-- Migration 0001 only added deleted_at to calendars and calendar_entries
+ALTER TABLE calendar_entry_links ADD COLUMN IF NOT EXISTS deleted_at TIMESTAMPTZ;
+ALTER TABLE calendar_shares ADD COLUMN IF NOT EXISTS deleted_at TIMESTAMPTZ;
+ALTER TABLE subtasks ADD COLUMN IF NOT EXISTS deleted_at TIMESTAMPTZ;
+ALTER TABLE resources ADD COLUMN IF NOT EXISTS deleted_at TIMESTAMPTZ;
+ALTER TABLE resource_bookings ADD COLUMN IF NOT EXISTS deleted_at TIMESTAMPTZ;
+-- Also add missing created_at/updated_at for tables that lacked them
+ALTER TABLE calendar_entry_links ADD COLUMN IF NOT EXISTS created_at TIMESTAMPTZ DEFAULT NOW();
+ALTER TABLE calendar_entry_links ADD COLUMN IF NOT EXISTS updated_at TIMESTAMPTZ DEFAULT NOW();
+ALTER TABLE calendar_shares ADD COLUMN IF NOT EXISTS created_at TIMESTAMPTZ DEFAULT NOW();
+ALTER TABLE calendar_shares ADD COLUMN IF NOT EXISTS updated_at TIMESTAMPTZ DEFAULT NOW();
+ALTER TABLE subtasks ADD COLUMN IF NOT EXISTS updated_at TIMESTAMPTZ DEFAULT NOW();
+ALTER TABLE resources ADD COLUMN IF NOT EXISTS created_at TIMESTAMPTZ DEFAULT NOW();
+ALTER TABLE resources ADD COLUMN IF NOT EXISTS updated_at TIMESTAMPTZ DEFAULT NOW();
+ALTER TABLE resource_bookings ADD COLUMN IF NOT EXISTS created_at TIMESTAMPTZ DEFAULT NOW();
+ALTER TABLE resource_bookings ADD COLUMN IF NOT EXISTS updated_at TIMESTAMPTZ DEFAULT NOW();

app/plugins/builtins/entity_links/migrations/0001_initial.sql

@@ -6,6 +6,7 @@ CREATE TABLE IF NOT EXISTS entity_links (
     entity_type VARCHAR(20) NOT NULL,
     entity_id UUID NOT NULL,
     created_by UUID,
+    deleted_at TIMESTAMPTZ,
     created_at TIMESTAMPTZ NOT NULL DEFAULT now(),
     updated_at TIMESTAMPTZ NOT NULL DEFAULT now(),
     CONSTRAINT uq_entity_links_file_entity UNIQUE (tenant_id, file_id, entity_type, entity_id)

app/plugins/builtins/entity_links/migrations/0002_add_deleted_at.sql

@@ -0,0 +1,3 @@
+-- Fix: EntityLink inherits TenantMixin -> SoftDeleteMixin (deleted_at)
+-- Migration 0001 did not include this column
+ALTER TABLE entity_links ADD COLUMN IF NOT EXISTS deleted_at TIMESTAMPTZ;

app/plugins/builtins/mail/migrations/0010_add_deleted_at.sql

@@ -0,0 +1,18 @@
+-- Fix: All mail models inherit TenantMixin -> SoftDeleteMixin (deleted_at)
+-- Migration 0001 did not include deleted_at on most tables; 0008 only fixed mail_sync_queue
+-- This migration adds deleted_at to all remaining mail tables
+ALTER TABLE mail_accounts ADD COLUMN IF NOT EXISTS deleted_at TIMESTAMPTZ;
+ALTER TABLE mail_folders ADD COLUMN IF NOT EXISTS deleted_at TIMESTAMPTZ;
+ALTER TABLE mails ADD COLUMN IF NOT EXISTS deleted_at TIMESTAMPTZ;
+ALTER TABLE mail_attachments ADD COLUMN IF NOT EXISTS deleted_at TIMESTAMPTZ;
+ALTER TABLE mail_labels ADD COLUMN IF NOT EXISTS deleted_at TIMESTAMPTZ;
+ALTER TABLE mail_label_assignments ADD COLUMN IF NOT EXISTS deleted_at TIMESTAMPTZ;
+ALTER TABLE mail_rules ADD COLUMN IF NOT EXISTS deleted_at TIMESTAMPTZ;
+ALTER TABLE mail_templates ADD COLUMN IF NOT EXISTS deleted_at TIMESTAMPTZ;
+ALTER TABLE mail_signatures ADD COLUMN IF NOT EXISTS deleted_at TIMESTAMPTZ;
+ALTER TABLE vacation_sent_log ADD COLUMN IF NOT EXISTS deleted_at TIMESTAMPTZ;
+ALTER TABLE mail_seen_by ADD COLUMN IF NOT EXISTS deleted_at TIMESTAMPTZ;
+ALTER TABLE mail_account_delegates ADD COLUMN IF NOT EXISTS deleted_at TIMESTAMPTZ;
+ALTER TABLE mail_account_send_permissions ADD COLUMN IF NOT EXISTS deleted_at TIMESTAMPTZ;
+ALTER TABLE pgp_keys ADD COLUMN IF NOT EXISTS deleted_at TIMESTAMPTZ;
+ALTER TABLE contact_pgp_keys ADD COLUMN IF NOT EXISTS deleted_at TIMESTAMPTZ;

app/plugins/builtins/mcp_client/migrations/0001_initial.sql

@@ -8,6 +8,7 @@ CREATE TABLE IF NOT EXISTS mcp_server_configs (
     description TEXT,
     last_connected_at TIMESTAMPTZ,
     created_by UUID,
+    deleted_at TIMESTAMPTZ,
     created_at TIMESTAMPTZ DEFAULT NOW(),
     updated_at TIMESTAMPTZ DEFAULT NOW()
 );

app/plugins/builtins/mcp_client/migrations/0002_add_deleted_at.sql

@@ -0,0 +1,3 @@
+-- Fix: McpServerConfig inherits TenantMixin -> SoftDeleteMixin (deleted_at)
+-- Migration 0001 did not include this column, causing queries to crash
+ALTER TABLE mcp_server_configs ADD COLUMN IF NOT EXISTS deleted_at TIMESTAMPTZ;

app/plugins/builtins/tags/migrations/0001_initial.sql

@@ -4,6 +4,7 @@ CREATE TABLE IF NOT EXISTS tags (
     tenant_id UUID NOT NULL,
     name VARCHAR(100) NOT NULL,
     color VARCHAR(7) NOT NULL DEFAULT '#6B7280',
+    deleted_at TIMESTAMPTZ,
     created_at TIMESTAMPTZ NOT NULL DEFAULT now(),
     updated_at TIMESTAMPTZ NOT NULL DEFAULT now(),
     CONSTRAINT uq_tags_tenant_name UNIQUE (tenant_id, name)
@@ -16,6 +17,7 @@ CREATE TABLE IF NOT EXISTS tag_assignments (
     tag_id UUID NOT NULL REFERENCES tags(id) ON DELETE CASCADE,
     entity_type VARCHAR(20) NOT NULL,
     entity_id UUID NOT NULL,
+    deleted_at TIMESTAMPTZ,
     created_at TIMESTAMPTZ NOT NULL DEFAULT now(),
     updated_at TIMESTAMPTZ NOT NULL DEFAULT now(),
     CONSTRAINT uq_tag_assignments_entity UNIQUE (tenant_id, tag_id, entity_type, entity_id)

app/plugins/builtins/tags/migrations/0002_add_deleted_at.sql

@@ -0,0 +1,4 @@
+-- Fix: Tag and TagAssignment inherit TenantMixin -> SoftDeleteMixin (deleted_at)
+-- Migration 0001 did not include this column, causing queries to crash
+ALTER TABLE tags ADD COLUMN IF NOT EXISTS deleted_at TIMESTAMPTZ;
+ALTER TABLE tag_assignments ADD COLUMN IF NOT EXISTS deleted_at TIMESTAMPTZ;

app/plugins/builtins/unified_search/migrations/0001_initial.sql

@@ -11,6 +11,7 @@ CREATE TABLE IF NOT EXISTS unified_search_providers (
     plugin_name VARCHAR(80) NOT NULL,
     is_active   BOOLEAN NOT NULL DEFAULT TRUE,
     config      JSONB NOT NULL DEFAULT '{}'::jsonb,
+    deleted_at  TIMESTAMPTZ,
     created_at  TIMESTAMPTZ NOT NULL DEFAULT now(),
     updated_at  TIMESTAMPTZ NOT NULL DEFAULT now(),
     UNIQUE(tenant_id, entity_type)
@@ -27,7 +28,9 @@ CREATE TABLE IF NOT EXISTS unified_search_index_log (
     action       VARCHAR(20) NOT NULL,
     status       VARCHAR(20) NOT NULL DEFAULT 'pending',
     error_message TEXT,
-    created_at   TIMESTAMPTZ NOT NULL DEFAULT now()
+    deleted_at   TIMESTAMPTZ,
+    created_at   TIMESTAMPTZ NOT NULL DEFAULT now(),
+    updated_at   TIMESTAMPTZ NOT NULL DEFAULT now()
 );
 
 CREATE INDEX IF NOT EXISTS ix_usil_tenant ON unified_search_index_log(tenant_id);

app/plugins/builtins/unified_search/migrations/0003_add_deleted_at.sql

@@ -0,0 +1,6 @@
+-- Fix: SearchProviderRegistry and SearchIndexLog inherit TenantMixin -> SoftDeleteMixin (deleted_at)
+-- Migration 0001 did not include this column
+ALTER TABLE unified_search_providers ADD COLUMN IF NOT EXISTS deleted_at TIMESTAMPTZ;
+ALTER TABLE unified_search_index_log ADD COLUMN IF NOT EXISTS deleted_at TIMESTAMPTZ;
+-- SearchIndexLog also needs updated_at (TimestampMixin)
+ALTER TABLE unified_search_index_log ADD COLUMN IF NOT EXISTS updated_at TIMESTAMPTZ NOT NULL DEFAULT now();