diff --git a/CHANGELOG.asciidoc b/CHANGELOG.asciidoc
index 6d3746b9a45..e6009606fba 100644
--- a/CHANGELOG.asciidoc
+++ b/CHANGELOG.asciidoc
@@ -47,6 +47,9 @@ https://github.com/elastic/beats/compare/v5.0.0-alpha5...master[Check the HEAD d
 - Fix Elasticsearch structured error response parsing error. {issue}2229[2229]
 - Fixed the run script to allow the overriding of the configuration file. {issue}2171[2171]
 - Fix logstash output crash if no hosts are configured. {issue}2325[2325]
+- Fix array value support in -E CLI flag. {pull}2521[2521]
+- Fix merging array values if -c CLI flag is used multiple times. {pull}2521[2521]
+- Fix beats failing to start due to invalid duplicate key error in configuration file. {pull}2521[2521]
 
 *Metricbeat*
 - Fix module filters to work properly with drop_event filter. {issue}2249[2249]
diff --git a/glide.yaml b/glide.yaml
index 9e068072522..706cdcb5574 100644
--- a/glide.yaml
+++ b/glide.yaml
@@ -75,7 +75,7 @@ import:
 - package: github.com/dustin/go-humanize
   version: 499693e27ee0d14ffab67c31ad065fdb3d34ea75
 - package: github.com/elastic/go-ucfg
-  version: v0.3.4
+  version: v0.3.6
 - package: github.com/armon/go-socks5
   version: 3a873e99f5400ad7706e464e905ffcc94b3ff247
 - package: github.com/pkg/errors
diff --git a/vendor/github.com/elastic/go-ucfg/CHANGELOG.md b/vendor/github.com/elastic/go-ucfg/CHANGELOG.md
index a4a376866d5..d7e45eb422e 100644
--- a/vendor/github.com/elastic/go-ucfg/CHANGELOG.md
+++ b/vendor/github.com/elastic/go-ucfg/CHANGELOG.md
@@ -14,6 +14,17 @@ This project adheres to [Semantic Versioning](http://semver.org/).
 
 ### Fixed
 
+## [0.3.6]
+
+### Fixed
+- Fix duplicate key error when normalizing tables. #63
+
+## [0.3.5]
+
+### Fixed
+- Fix merging array values. #59
+- Fix initializing empty array values. #58
+
 ## [0.3.4]
 
 ### Fixed
@@ -100,7 +111,9 @@ This project adheres to [Semantic Versioning](http://semver.org/).
 - Introduced CHANGELOG.md for documenting changes to ucfg.
 
 
-[Unreleased]: https://github.com/elastic/go-ucfg/compare/v0.3.4...HEAD
+[Unreleased]: https://github.com/elastic/go-ucfg/compare/v0.3.6...HEAD
+[0.3.6]: https://github.com/elastic/go-ucfg/compare/v0.3.5...v0.3.6
+[0.3.5]: https://github.com/elastic/go-ucfg/compare/v0.3.4...v0.3.5
 [0.3.4]: https://github.com/elastic/go-ucfg/compare/v0.3.3...v0.3.4
 [0.3.3]: https://github.com/elastic/go-ucfg/compare/v0.3.2...v0.3.3
 [0.3.2]: https://github.com/elastic/go-ucfg/compare/v0.3.1...v0.3.2
diff --git a/vendor/github.com/elastic/go-ucfg/README.md b/vendor/github.com/elastic/go-ucfg/README.md
index 16f110abcb8..7a5c962820a 100644
--- a/vendor/github.com/elastic/go-ucfg/README.md
+++ b/vendor/github.com/elastic/go-ucfg/README.md
@@ -81,4 +81,4 @@ The above uses `Counter` as the config variable. ucfg assures that the value is
 
 ucfg has the following requirements:
 
-* Golang 1.6
+* Golang 1.5+
diff --git a/vendor/github.com/elastic/go-ucfg/merge.go b/vendor/github.com/elastic/go-ucfg/merge.go
index f3085c8a9dc..b1851c78202 100644
--- a/vendor/github.com/elastic/go-ucfg/merge.go
+++ b/vendor/github.com/elastic/go-ucfg/merge.go
@@ -10,6 +10,7 @@ import (
 func (c *Config) Merge(from interface{}, options ...Option) error {
 	opts := makeOptions(options)
 	other, err := normalize(opts, from)
+
 	if err != nil {
 		return err
 	}
@@ -17,6 +18,13 @@ func (c *Config) Merge(from interface{}, options ...Option) error {
 }
 
 func mergeConfig(opts *options, to, from *Config) Error {
+	if err := mergeConfigDict(opts, to, from); err != nil {
+		return err
+	}
+	return mergeConfigArr(opts, to, from)
+}
+
+func mergeConfigDict(opts *options, to, from *Config) Error {
 	for k, v := range from.fields.dict() {
 		ctx := context{
 			parent: cfgSub{to},
@@ -48,6 +56,56 @@ func mergeConfig(opts *options, to, from *Config) Error {
 	return nil
 }
 
+func mergeConfigArr(opts *options, to, from *Config) Error {
+	l := len(to.fields.array())
+	if l > len(from.fields.array()) {
+		l = len(from.fields.array())
+	}
+
+	// merge array indexes available in to and from
+	for i := 0; i < l; i++ {
+		ctx := context{
+			parent: cfgSub{to},
+			field:  fmt.Sprintf("%v", i),
+		}
+
+		v := from.fields.array()[i]
+
+		old := to.fields.array()[i]
+		subOld, err := old.toConfig(opts)
+		if err != nil {
+			to.fields.setAt(i, cfgSub{to}, v.cpy(ctx))
+			continue
+		}
+
+		subFrom, err := v.toConfig(opts)
+		if err != nil {
+			to.fields.setAt(i, cfgSub{to}, v.cpy(ctx))
+		}
+
+		if err := mergeConfig(opts, subOld, subFrom); err != nil {
+			return err
+		}
+	}
+
+	end := len(from.fields.array())
+	if end <= l {
+		return nil
+	}
+
+	// add additional array entries not yet in 'to'
+	for ; l < end; l++ {
+		ctx := context{
+			parent: cfgSub{to},
+			field:  fmt.Sprintf("%v", l),
+		}
+		v := from.fields.array()[l]
+		to.fields.setAt(l, cfgSub{to}, v.cpy(ctx))
+	}
+
+	return nil
+}
+
 // convert from into normalized *Config checking for errors
 // before merging generated(normalized) config with current config
 func normalize(opts *options, from interface{}) (*Config, Error) {
@@ -166,14 +224,19 @@ func normalizeSetField(
 		}
 		old = nil
 	}
-	if old != nil {
-		if _, isNil := val.(*cfgNil); val == nil || isNil {
-			return nil
-		}
+
+	switch {
+	case !isNil(old) && isNil(val):
+		return nil
+	case isNil(old):
+		return p.SetValue(cfg, opts, val)
+	case isSub(old) && isSub(val):
+		cfgOld, _ := old.toConfig(opts)
+		cfgVal, _ := val.toConfig(opts)
+		return mergeConfig(opts, cfgOld, cfgVal)
+	default:
 		return raiseDuplicateKey(cfg, name)
 	}
-
-	return p.SetValue(cfg, opts, val)
 }
 
 func normalizeStructValue(opts *options, ctx context, from reflect.Value) (value, Error) {
diff --git a/vendor/github.com/elastic/go-ucfg/path.go b/vendor/github.com/elastic/go-ucfg/path.go
index 2efc606a85d..0e0e85d3a88 100644
--- a/vendor/github.com/elastic/go-ucfg/path.go
+++ b/vendor/github.com/elastic/go-ucfg/path.go
@@ -45,23 +45,25 @@ func parsePath(in, sep string) cfgPath {
 	if sep == "" {
 		return cfgPath{
 			sep:    sep,
-			fields: []field{namedField{in}},
+			fields: []field{parseField(in)},
 		}
 	}
 
 	elems := strings.Split(in, sep)
 	fields := make([]field, 0, len(elems))
 	for _, elem := range elems {
-		if idx, err := strconv.ParseInt(elem, 0, 64); err == nil {
-			fields = append(fields, idxField{int(idx)})
-		} else {
-			fields = append(fields, namedField{elem})
-		}
+		fields = append(fields, parseField(elem))
 	}
-
 	return cfgPath{fields: fields, sep: sep}
 }
 
+func parseField(in string) field {
+	if idx, err := strconv.ParseInt(in, 0, 64); err == nil {
+		return idxField{int(idx)}
+	}
+	return namedField{in}
+}
+
 func (p cfgPath) String() string {
 	if len(p.fields) == 0 {
 		return ""
@@ -159,7 +161,7 @@ func (p cfgPath) SetValue(cfg *Config, opt *options, val value) Error {
 			return err
 		}
 
-		if _, isNil := v.(*cfgNil); v == nil || isNil {
+		if isNil(v) {
 			break
 		}
 		node = v
@@ -200,7 +202,7 @@ func (i idxField) SetValue(opts *options, elem value, v value) Error {
 		return raiseExpectedObject(opts, elem)
 	}
 
-	sub.c.fields.setAt(i.i, v)
+	sub.c.fields.setAt(i.i, elem, v)
 	v.SetContext(context{parent: elem, field: i.String()})
 	return nil
 }
diff --git a/vendor/github.com/elastic/go-ucfg/reify.go b/vendor/github.com/elastic/go-ucfg/reify.go
index 755bb3dad07..bc2fc2aeca2 100644
--- a/vendor/github.com/elastic/go-ucfg/reify.go
+++ b/vendor/github.com/elastic/go-ucfg/reify.go
@@ -170,7 +170,7 @@ func reifyGetField(
 		value = nil
 	}
 
-	if _, ok := value.(*cfgNil); value == nil || ok {
+	if isNil(value) {
 		if err := runValidators(nil, opts.validators); err != nil {
 			return raiseValidation(cfg.ctx, cfg.metadata, name, err)
 		}
@@ -430,7 +430,7 @@ func reifyPrimitive(
 	t, baseType reflect.Type,
 ) (reflect.Value, Error) {
 	// zero initialize value if val==nil
-	if _, ok := val.(*cfgNil); ok {
+	if isNil(val) {
 		return pointerize(t, baseType, reflect.Zero(baseType)), nil
 	}
 
diff --git a/vendor/github.com/elastic/go-ucfg/types.go b/vendor/github.com/elastic/go-ucfg/types.go
index 230262f4afc..4df7621554d 100644
--- a/vendor/github.com/elastic/go-ucfg/types.go
+++ b/vendor/github.com/elastic/go-ucfg/types.go
@@ -297,7 +297,7 @@ func (c cfgSub) cpy(ctx context) value {
 		for i, f := range arr {
 			ctx := f.Context()
 			v := f.cpy(context{field: ctx.field, parent: newC})
-			fields.setAt(i, v)
+			fields.setAt(i, newC, v)
 		}
 	}
 
@@ -503,3 +503,19 @@ func (s *cfgSplice) toFloat(opt *options) (float64, error) {
 	}
 	return strconv.ParseFloat(str, 64)
 }
+
+func isNil(v value) bool {
+	if v == nil {
+		return true
+	}
+	_, tst := v.(*cfgNil)
+	return tst
+}
+
+func isSub(v value) bool {
+	if v == nil {
+		return false
+	}
+	_, tst := v.(cfgSub)
+	return tst
+}
diff --git a/vendor/github.com/elastic/go-ucfg/ucfg.go b/vendor/github.com/elastic/go-ucfg/ucfg.go
index 9e44d4beaf6..9972f20f91b 100644
--- a/vendor/github.com/elastic/go-ucfg/ucfg.go
+++ b/vendor/github.com/elastic/go-ucfg/ucfg.go
@@ -1,6 +1,7 @@
 package ucfg
 
 import (
+	"fmt"
 	"reflect"
 	"regexp"
 	"time"
@@ -138,11 +139,19 @@ func (f *fields) add(v value) {
 	f.a = append(f.a, v)
 }
 
-func (f *fields) setAt(idx int, v value) {
-	if idx >= len(f.a) {
+func (f *fields) setAt(idx int, parent, v value) {
+	l := len(f.a)
+	if idx >= l {
 		tmp := make([]value, idx+1)
 		copy(tmp, f.a)
+
+		for i := l; i < idx; i++ {
+			ctx := context{parent: parent, field: fmt.Sprintf("%d", i)}
+			tmp[i] = &cfgNil{cfgPrimitive{ctx, nil}}
+		}
+
 		f.a = tmp
 	}
+
 	f.a[idx] = v
 }