refactor(repo): consolidate openflare-server to root and move subprojects to internal/apps

- Merge all files inside openflare-server to the repository root directory.
- Relocate agent, relay, and flared subprojects from internal/ to internal/apps/.
- Combine docker-compose files and update build context paths to root.
- Update GitHub workflows and Dockerfiles to refer to new directories and package names.
- Rewrite Go package imports across all files.
- Resolve database renew test race condition and clean up docs.

internal/apps/agent/config/duration.go

@@ -0,0 +1,54 @@
+package config
+
+import (
+	"encoding/json"
+	"fmt"
+	"strconv"
+	"strings"
+	"time"
+)
+
+type MillisecondDuration time.Duration
+
+func (d MillisecondDuration) Duration() time.Duration {
+	return time.Duration(d)
+}
+
+func (d MillisecondDuration) String() string {
+	return time.Duration(d).String()
+}
+
+func (d *MillisecondDuration) UnmarshalJSON(data []byte) error {
+	raw := strings.TrimSpace(string(data))
+	if raw == "" || raw == "null" {
+		*d = 0
+		return nil
+	}
+	if strings.HasPrefix(raw, "\"") {
+		var text string
+		if err := json.Unmarshal(data, &text); err != nil {
+			return err
+		}
+		text = strings.TrimSpace(text)
+		if text == "" {
+			*d = 0
+			return nil
+		}
+		parsed, err := time.ParseDuration(text)
+		if err != nil {
+			return fmt.Errorf("invalid duration string %q: %w", text, err)
+		}
+		*d = MillisecondDuration(parsed)
+		return nil
+	}
+	ms, err := strconv.ParseInt(raw, 10, 64)
+	if err != nil {
+		return fmt.Errorf("invalid duration milliseconds %q: %w", raw, err)
+	}
+	*d = MillisecondDuration(time.Duration(ms) * time.Millisecond)
+	return nil
+}
+
+func (d MillisecondDuration) MarshalJSON() ([]byte, error) {
+	return json.Marshal(time.Duration(d).Milliseconds())
+}