Reorganize repo: backend/, deploy/, docs/ layout + AGENTS.md

Restructure the monorepo into clear top-level directories:
- backend/: Go module root (cmd, internal, pkg, configs, migrations,
  docs/swagger, scripts, tests, go.mod, Makefile, .air.toml)
- deploy/: Docker (Dockerfile, docker-compose*), quickstart, fluentd
- docs/: project documentation + reports/ (moved from repo root)
- AGENTS.md: new AI coding-agent guide at repo root

Update all references to the new layout:
- Dockerfile: COPY backend/go.mod, COPY backend/ (context = repo root)
- docker-compose files: context ../.., dockerfile deploy/docker/Dockerfile,
  env_file ../../.env, volume mounts ../../backend:/app
- deploy/quickstart/compose.yaml: dockerfile deploy/docker/Dockerfile
- CI: working-directory: backend for go commands, file deploy/docker/Dockerfile,
  coverage path backend/coverage.out, health_check backend/scripts/
- backend/Makefile: docker target uses -f ../deploy/docker/Dockerfile ../
- README: architecture tree, quickstart, config paths updated

Move root stray scripts (rename_models.*, run_m11_tests.sh, verify_build.sh,
gorm_bool_main.go) to backend/scripts/legacy/. All moves via git mv to
preserve history. Build, vet, SQLite tests, and docker compose config verified.

backend/migrations/000018_add_conversation_message_parity_fields.up.sql

@@ -0,0 +1,37 @@
+ALTER TABLE conversations ADD COLUMN IF NOT EXISTS display_id INTEGER;
+ALTER TABLE conversations ADD COLUMN IF NOT EXISTS contact_inbox_id INTEGER;
+ALTER TABLE conversations ADD COLUMN IF NOT EXISTS assignee_agent_bot_id INTEGER;
+ALTER TABLE conversations ADD COLUMN IF NOT EXISTS team_id INTEGER;
+ALTER TABLE conversations ADD COLUMN IF NOT EXISTS campaign_id INTEGER;
+ALTER TABLE conversations ADD COLUMN IF NOT EXISTS sla_policy_id INTEGER;
+ALTER TABLE conversations ADD COLUMN IF NOT EXISTS snoozed_until BIGINT;
+ALTER TABLE conversations ADD COLUMN IF NOT EXISTS additional_attributes JSONB DEFAULT '{}';
+ALTER TABLE conversations ADD COLUMN IF NOT EXISTS custom_attributes JSONB DEFAULT '{}';
+ALTER TABLE conversations ADD COLUMN IF NOT EXISTS agent_last_seen_at BIGINT;
+ALTER TABLE conversations ADD COLUMN IF NOT EXISTS assignee_last_seen_at BIGINT;
+ALTER TABLE conversations ADD COLUMN IF NOT EXISTS contact_last_seen_at BIGINT;
+ALTER TABLE conversations ADD COLUMN IF NOT EXISTS waiting_since BIGINT;
+ALTER TABLE conversations ADD COLUMN IF NOT EXISTS last_activity_at BIGINT;
+ALTER TABLE conversations ADD COLUMN IF NOT EXISTS first_reply_created_at BIGINT;
+ALTER TABLE conversations ADD COLUMN IF NOT EXISTS last_non_sys_msg_at BIGINT;
+ALTER TABLE conversations ADD COLUMN IF NOT EXISTS muted BOOLEAN DEFAULT FALSE;
+ALTER TABLE conversations ADD COLUMN IF NOT EXISTS resolved_at TIMESTAMP WITH TIME ZONE;
+ALTER TABLE conversations ADD COLUMN IF NOT EXISTS resumed_at TIMESTAMP WITH TIME ZONE;
+
+ALTER TABLE messages ADD COLUMN IF NOT EXISTS status VARCHAR(50) DEFAULT 'sent';
+ALTER TABLE messages ADD COLUMN IF NOT EXISTS echo_id VARCHAR(255);
+ALTER TABLE messages ADD COLUMN IF NOT EXISTS content_attributes JSONB DEFAULT '{}';
+ALTER TABLE messages ADD COLUMN IF NOT EXISTS additional_attributes JSONB DEFAULT '{}';
+ALTER TABLE messages ADD COLUMN IF NOT EXISTS external_source_ids JSONB DEFAULT '{}';
+
+UPDATE conversations
+SET display_id = numbered.display_id
+FROM (
+  SELECT id, ROW_NUMBER() OVER (PARTITION BY account_id ORDER BY id)::integer AS display_id
+  FROM conversations
+  WHERE display_id IS NULL OR display_id = 0
+) AS numbered
+WHERE conversations.id = numbered.id;
+
+CREATE INDEX IF NOT EXISTS idx_conversations_account_display_id ON conversations(account_id, display_id) WHERE deleted_at IS NULL;
+CREATE INDEX IF NOT EXISTS idx_messages_echo_id ON messages(echo_id) WHERE deleted_at IS NULL;