diff --git a/docs/docs/references/configuration/cli/trivy_aws.md b/docs/docs/references/configuration/cli/trivy_aws.md
index aa0255a7ebcd..fad5d106bc16 100644
--- a/docs/docs/references/configuration/cli/trivy_aws.md
+++ b/docs/docs/references/configuration/cli/trivy_aws.md
@@ -89,7 +89,7 @@ trivy aws [flags]
       --ignorefile string                 specify .trivyignore file (default ".trivyignore")
       --include-deprecated-checks         include deprecated checks
       --include-non-failures              include successes and exceptions, available with '--scanners misconfig'
-      --list-all-pkgs                     enabling the option will output all packages regardless of vulnerability
+      --list-all-pkgs                     output all packages in the JSON report regardless of vulnerability
       --max-cache-age duration            The maximum age of the cloud cache. Cached data will be required from the cloud provider if it is older than this. (default 24h0m0s)
       --misconfig-scanners strings        comma-separated list of misconfig scanners to use for misconfiguration scanning (default [azure-arm,cloudformation,dockerfile,helm,kubernetes,terraform,terraformplan-json,terraformplan-snapshot])
   -o, --output string                     output file name
diff --git a/docs/docs/references/configuration/cli/trivy_convert.md b/docs/docs/references/configuration/cli/trivy_convert.md
index e8fe589500ea..d76d303e3b03 100644
--- a/docs/docs/references/configuration/cli/trivy_convert.md
+++ b/docs/docs/references/configuration/cli/trivy_convert.md
@@ -26,7 +26,7 @@ trivy convert [flags] RESULT_JSON
   -h, --help                       help for convert
       --ignore-policy string       specify the Rego file path to evaluate each vulnerability
       --ignorefile string          specify .trivyignore file (default ".trivyignore")
-      --list-all-pkgs              enabling the option will output all packages regardless of vulnerability
+      --list-all-pkgs              output all packages in the JSON report regardless of vulnerability
   -o, --output string              output file name
       --output-plugin-arg string   [EXPERIMENTAL] output plugin arguments
       --report string              specify a report format for the output (all,summary) (default "all")
diff --git a/docs/docs/references/configuration/cli/trivy_filesystem.md b/docs/docs/references/configuration/cli/trivy_filesystem.md
index e79b923e3786..4d90f4e87e63 100644
--- a/docs/docs/references/configuration/cli/trivy_filesystem.md
+++ b/docs/docs/references/configuration/cli/trivy_filesystem.md
@@ -55,7 +55,7 @@ trivy filesystem [flags] PATH
       --java-db-repository string         OCI repository to retrieve trivy-java-db from (default "ghcr.io/aquasecurity/trivy-java-db:1")
       --license-confidence-level float    specify license classifier's confidence level (default 0.9)
       --license-full                      eagerly look for licenses in source code headers and license files
-      --list-all-pkgs                     enabling the option will output all packages regardless of vulnerability
+      --list-all-pkgs                     output all packages in the JSON report regardless of vulnerability
       --misconfig-scanners strings        comma-separated list of misconfig scanners to use for misconfiguration scanning (default [azure-arm,cloudformation,dockerfile,helm,kubernetes,terraform,terraformplan-json,terraformplan-snapshot])
       --module-dir string                 specify directory to the wasm modules that will be loaded (default "$HOME/.trivy/modules")
       --no-progress                       suppress progress bar
diff --git a/docs/docs/references/configuration/cli/trivy_image.md b/docs/docs/references/configuration/cli/trivy_image.md
index 980cf68a795f..c61c6b648d7c 100644
--- a/docs/docs/references/configuration/cli/trivy_image.md
+++ b/docs/docs/references/configuration/cli/trivy_image.md
@@ -73,7 +73,7 @@ trivy image [flags] IMAGE_NAME
       --java-db-repository string         OCI repository to retrieve trivy-java-db from (default "ghcr.io/aquasecurity/trivy-java-db:1")
       --license-confidence-level float    specify license classifier's confidence level (default 0.9)
       --license-full                      eagerly look for licenses in source code headers and license files
-      --list-all-pkgs                     enabling the option will output all packages regardless of vulnerability
+      --list-all-pkgs                     output all packages in the JSON report regardless of vulnerability
       --misconfig-scanners strings        comma-separated list of misconfig scanners to use for misconfiguration scanning (default [azure-arm,cloudformation,dockerfile,helm,kubernetes,terraform,terraformplan-json,terraformplan-snapshot])
       --module-dir string                 specify directory to the wasm modules that will be loaded (default "$HOME/.trivy/modules")
       --no-progress                       suppress progress bar
diff --git a/docs/docs/references/configuration/cli/trivy_kubernetes.md b/docs/docs/references/configuration/cli/trivy_kubernetes.md
index edd2efe6c5de..54dc2db07f75 100644
--- a/docs/docs/references/configuration/cli/trivy_kubernetes.md
+++ b/docs/docs/references/configuration/cli/trivy_kubernetes.md
@@ -69,7 +69,7 @@ trivy kubernetes [flags] [CONTEXT]
       --java-db-repository string         OCI repository to retrieve trivy-java-db from (default "ghcr.io/aquasecurity/trivy-java-db:1")
       --k8s-version string                specify k8s version to validate outdated api by it (example: 1.21.0)
       --kubeconfig string                 specify the kubeconfig file path to use
-      --list-all-pkgs                     enabling the option will output all packages regardless of vulnerability
+      --list-all-pkgs                     output all packages in the JSON report regardless of vulnerability
       --misconfig-scanners strings        comma-separated list of misconfig scanners to use for misconfiguration scanning (default [azure-arm,cloudformation,dockerfile,helm,kubernetes,terraform,terraformplan-json,terraformplan-snapshot])
       --no-progress                       suppress progress bar
       --node-collector-imageref string    indicate the image reference for the node-collector scan job (default "ghcr.io/aquasecurity/node-collector:0.2.1")
diff --git a/docs/docs/references/configuration/cli/trivy_repository.md b/docs/docs/references/configuration/cli/trivy_repository.md
index 7efde1657cc7..4f73c0d4e13d 100644
--- a/docs/docs/references/configuration/cli/trivy_repository.md
+++ b/docs/docs/references/configuration/cli/trivy_repository.md
@@ -55,7 +55,7 @@ trivy repository [flags] (REPO_PATH | REPO_URL)
       --java-db-repository string         OCI repository to retrieve trivy-java-db from (default "ghcr.io/aquasecurity/trivy-java-db:1")
       --license-confidence-level float    specify license classifier's confidence level (default 0.9)
       --license-full                      eagerly look for licenses in source code headers and license files
-      --list-all-pkgs                     enabling the option will output all packages regardless of vulnerability
+      --list-all-pkgs                     output all packages in the JSON report regardless of vulnerability
       --misconfig-scanners strings        comma-separated list of misconfig scanners to use for misconfiguration scanning (default [azure-arm,cloudformation,dockerfile,helm,kubernetes,terraform,terraformplan-json,terraformplan-snapshot])
       --module-dir string                 specify directory to the wasm modules that will be loaded (default "$HOME/.trivy/modules")
       --no-progress                       suppress progress bar
diff --git a/docs/docs/references/configuration/cli/trivy_rootfs.md b/docs/docs/references/configuration/cli/trivy_rootfs.md
index ea6a3093802f..6f264b5c2362 100644
--- a/docs/docs/references/configuration/cli/trivy_rootfs.md
+++ b/docs/docs/references/configuration/cli/trivy_rootfs.md
@@ -57,7 +57,7 @@ trivy rootfs [flags] ROOTDIR
       --java-db-repository string         OCI repository to retrieve trivy-java-db from (default "ghcr.io/aquasecurity/trivy-java-db:1")
       --license-confidence-level float    specify license classifier's confidence level (default 0.9)
       --license-full                      eagerly look for licenses in source code headers and license files
-      --list-all-pkgs                     enabling the option will output all packages regardless of vulnerability
+      --list-all-pkgs                     output all packages in the JSON report regardless of vulnerability
       --misconfig-scanners strings        comma-separated list of misconfig scanners to use for misconfiguration scanning (default [azure-arm,cloudformation,dockerfile,helm,kubernetes,terraform,terraformplan-json,terraformplan-snapshot])
       --module-dir string                 specify directory to the wasm modules that will be loaded (default "$HOME/.trivy/modules")
       --no-progress                       suppress progress bar
diff --git a/docs/docs/references/configuration/cli/trivy_sbom.md b/docs/docs/references/configuration/cli/trivy_sbom.md
index 5d941e9744ba..d5c4030d7281 100644
--- a/docs/docs/references/configuration/cli/trivy_sbom.md
+++ b/docs/docs/references/configuration/cli/trivy_sbom.md
@@ -39,7 +39,7 @@ trivy sbom [flags] SBOM_PATH
       --ignored-licenses strings    specify a list of license to ignore
       --ignorefile string           specify .trivyignore file (default ".trivyignore")
       --java-db-repository string   OCI repository to retrieve trivy-java-db from (default "ghcr.io/aquasecurity/trivy-java-db:1")
-      --list-all-pkgs               enabling the option will output all packages regardless of vulnerability
+      --list-all-pkgs               output all packages in the JSON report regardless of vulnerability
       --no-progress                 suppress progress bar
       --offline-scan                do not issue API requests to identify dependencies
   -o, --output string               output file name
diff --git a/docs/docs/references/configuration/cli/trivy_vm.md b/docs/docs/references/configuration/cli/trivy_vm.md
index fc9b536a418d..51b7ad43cf38 100644
--- a/docs/docs/references/configuration/cli/trivy_vm.md
+++ b/docs/docs/references/configuration/cli/trivy_vm.md
@@ -49,7 +49,7 @@ trivy vm [flags] VM_IMAGE
       --ignorefile string                 specify .trivyignore file (default ".trivyignore")
       --include-non-failures              include successes and exceptions, available with '--scanners misconfig'
       --java-db-repository string         OCI repository to retrieve trivy-java-db from (default "ghcr.io/aquasecurity/trivy-java-db:1")
-      --list-all-pkgs                     enabling the option will output all packages regardless of vulnerability
+      --list-all-pkgs                     output all packages in the JSON report regardless of vulnerability
       --misconfig-scanners strings        comma-separated list of misconfig scanners to use for misconfiguration scanning (default [azure-arm,cloudformation,dockerfile,helm,kubernetes,terraform,terraformplan-json,terraformplan-snapshot])
       --module-dir string                 specify directory to the wasm modules that will be loaded (default "$HOME/.trivy/modules")
       --no-progress                       suppress progress bar
diff --git a/integration/client_server_test.go b/integration/client_server_test.go
index 32ef4a972d26..a8a5f83f6941 100644
--- a/integration/client_server_test.go
+++ b/integration/client_server_test.go
@@ -39,10 +39,10 @@ type csArgs struct {
 
 func TestClientServer(t *testing.T) {
 	tests := []struct {
-		name    string
-		args    csArgs
-		golden  string
-		wantErr string
+		name     string
+		args     csArgs
+		golden   string
+		override func(t *testing.T, want, got *types.Report)
 	}{
 		{
 			name: "alpine 3.9",
@@ -270,6 +270,9 @@ func TestClientServer(t *testing.T) {
 				Target:           "https://github.com/knqyf263/trivy-ci-test",
 			},
 			golden: "testdata/test-repo.json.golden",
+			override: func(t *testing.T, want, got *types.Report) {
+				want.ArtifactName = "https://github.com/knqyf263/trivy-ci-test"
+			},
 		},
 	}
 
@@ -284,7 +287,7 @@ func TestClientServer(t *testing.T) {
 			}
 
 			runTest(t, osArgs, tt.golden, "", types.FormatJSON, runOptions{
-				override: overrideUID,
+				override: overrideFuncs(overrideUID, tt.override),
 			})
 		})
 	}
diff --git a/integration/repo_test.go b/integration/repo_test.go
index 00665f17ab8d..e11e5a21a8b4 100644
--- a/integration/repo_test.go
+++ b/integration/repo_test.go
@@ -234,6 +234,14 @@ func TestRepository(t *testing.T) {
 			},
 			golden: "testdata/composer.lock.json.golden",
 		},
+		{
+			name: "multiple lockfiles",
+			args: args{
+				scanner: types.VulnerabilityScanner,
+				input:   "testdata/fixtures/repo/trivy-ci-test",
+			},
+			golden: "testdata/test-repo.json.golden",
+		},
 		{
 			name: "dockerfile",
 			args: args{
diff --git a/integration/testdata/fixtures/repo/trivy-ci-test/Cargo.lock b/integration/testdata/fixtures/repo/trivy-ci-test/Cargo.lock
new file mode 100644
index 000000000000..ca70dc137dd5
--- /dev/null
+++ b/integration/testdata/fixtures/repo/trivy-ci-test/Cargo.lock
@@ -0,0 +1,666 @@
+# It is not intended for manual editing.
+[[package]]
+name = "ammonia"
+version = "1.9.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+dependencies = [
+ "html5ever 0.23.0 (registry+https://github.com/rust-lang/crates.io-index)",
+ "lazy_static 1.3.0 (registry+https://github.com/rust-lang/crates.io-index)",
+ "maplit 1.0.1 (registry+https://github.com/rust-lang/crates.io-index)",
+ "matches 0.1.8 (registry+https://github.com/rust-lang/crates.io-index)",
+ "tendril 0.4.1 (registry+https://github.com/rust-lang/crates.io-index)",
+ "url 1.7.2 (registry+https://github.com/rust-lang/crates.io-index)",
+]
+
+[[package]]
+name = "autocfg"
+version = "0.1.2"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+
+[[package]]
+name = "bitflags"
+version = "0.7.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+
+[[package]]
+name = "bitflags"
+version = "1.0.4"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+
+[[package]]
+name = "cfg-if"
+version = "0.1.7"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+
+[[package]]
+name = "cloudabi"
+version = "0.0.3"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+dependencies = [
+ "bitflags 1.0.4 (registry+https://github.com/rust-lang/crates.io-index)",
+]
+
+[[package]]
+name = "fuchsia-cprng"
+version = "0.1.1"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+
+[[package]]
+name = "futf"
+version = "0.1.4"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+dependencies = [
+ "mac 0.1.1 (registry+https://github.com/rust-lang/crates.io-index)",
+ "new_debug_unreachable 1.0.3 (registry+https://github.com/rust-lang/crates.io-index)",
+]
+
+[[package]]
+name = "gdi32-sys"
+version = "0.2.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+dependencies = [
+ "winapi 0.2.8 (registry+https://github.com/rust-lang/crates.io-index)",
+ "winapi-build 0.1.1 (registry+https://github.com/rust-lang/crates.io-index)",
+]
+
+[[package]]
+name = "html5ever"
+version = "0.23.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+dependencies = [
+ "log 0.4.6 (registry+https://github.com/rust-lang/crates.io-index)",
+ "mac 0.1.1 (registry+https://github.com/rust-lang/crates.io-index)",
+ "markup5ever 0.8.1 (registry+https://github.com/rust-lang/crates.io-index)",
+ "proc-macro2 0.4.30 (registry+https://github.com/rust-lang/crates.io-index)",
+ "quote 0.6.12 (registry+https://github.com/rust-lang/crates.io-index)",
+ "syn 0.15.34 (registry+https://github.com/rust-lang/crates.io-index)",
+]
+
+[[package]]
+name = "idna"
+version = "0.1.5"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+dependencies = [
+ "matches 0.1.8 (registry+https://github.com/rust-lang/crates.io-index)",
+ "unicode-bidi 0.3.4 (registry+https://github.com/rust-lang/crates.io-index)",
+ "unicode-normalization 0.1.8 (registry+https://github.com/rust-lang/crates.io-index)",
+]
+
+[[package]]
+name = "itoa"
+version = "0.4.4"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+
+[[package]]
+name = "kernel32-sys"
+version = "0.2.2"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+dependencies = [
+ "winapi 0.2.8 (registry+https://github.com/rust-lang/crates.io-index)",
+ "winapi-build 0.1.1 (registry+https://github.com/rust-lang/crates.io-index)",
+]
+
+[[package]]
+name = "lazy_static"
+version = "0.2.11"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+
+[[package]]
+name = "lazy_static"
+version = "1.3.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+
+[[package]]
+name = "libc"
+version = "0.2.54"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+
+[[package]]
+name = "libressl-pnacl-sys"
+version = "2.1.6"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+dependencies = [
+ "pnacl-build-helper 1.4.11 (registry+https://github.com/rust-lang/crates.io-index)",
+]
+
+[[package]]
+name = "log"
+version = "0.4.6"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+dependencies = [
+ "cfg-if 0.1.7 (registry+https://github.com/rust-lang/crates.io-index)",
+]
+
+[[package]]
+name = "mac"
+version = "0.1.1"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+
+[[package]]
+name = "maplit"
+version = "1.0.1"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+
+[[package]]
+name = "markup5ever"
+version = "0.8.1"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+dependencies = [
+ "log 0.4.6 (registry+https://github.com/rust-lang/crates.io-index)",
+ "phf 0.7.24 (registry+https://github.com/rust-lang/crates.io-index)",
+ "phf_codegen 0.7.24 (registry+https://github.com/rust-lang/crates.io-index)",
+ "serde 1.0.91 (registry+https://github.com/rust-lang/crates.io-index)",
+ "serde_derive 1.0.91 (registry+https://github.com/rust-lang/crates.io-index)",
+ "serde_json 1.0.39 (registry+https://github.com/rust-lang/crates.io-index)",
+ "string_cache 0.7.3 (registry+https://github.com/rust-lang/crates.io-index)",
+ "string_cache_codegen 0.4.2 (registry+https://github.com/rust-lang/crates.io-index)",
+ "tendril 0.4.1 (registry+https://github.com/rust-lang/crates.io-index)",
+]
+
+[[package]]
+name = "matches"
+version = "0.1.8"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+
+[[package]]
+name = "new_debug_unreachable"
+version = "1.0.3"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+
+[[package]]
+name = "normal"
+version = "0.1.0"
+dependencies = [
+ "ammonia 2.0.0 (registry+https://github.com/rust-lang/crates.io-index)",
+ "libc 0.2.54 (registry+https://github.com/rust-lang/crates.io-index)",
+ "openssl 0.8.3 (registry+https://github.com/rust-lang/crates.io-index)",
+]
+
+[[package]]
+name = "openssl"
+version = "0.8.3"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+dependencies = [
+ "bitflags 0.7.0 (registry+https://github.com/rust-lang/crates.io-index)",
+ "lazy_static 0.2.11 (registry+https://github.com/rust-lang/crates.io-index)",
+ "libc 0.2.54 (registry+https://github.com/rust-lang/crates.io-index)",
+ "openssl-sys 0.7.17 (registry+https://github.com/rust-lang/crates.io-index)",
+]
+
+[[package]]
+name = "openssl-sys"
+version = "0.7.17"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+dependencies = [
+ "gdi32-sys 0.2.0 (registry+https://github.com/rust-lang/crates.io-index)",
+ "libc 0.2.54 (registry+https://github.com/rust-lang/crates.io-index)",
+ "libressl-pnacl-sys 2.1.6 (registry+https://github.com/rust-lang/crates.io-index)",
+ "pkg-config 0.3.14 (registry+https://github.com/rust-lang/crates.io-index)",
+ "user32-sys 0.2.0 (registry+https://github.com/rust-lang/crates.io-index)",
+]
+
+[[package]]
+name = "percent-encoding"
+version = "1.0.1"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+
+[[package]]
+name = "phf"
+version = "0.7.24"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+dependencies = [
+ "phf_shared 0.7.24 (registry+https://github.com/rust-lang/crates.io-index)",
+]
+
+[[package]]
+name = "phf_codegen"
+version = "0.7.24"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+dependencies = [
+ "phf_generator 0.7.24 (registry+https://github.com/rust-lang/crates.io-index)",
+ "phf_shared 0.7.24 (registry+https://github.com/rust-lang/crates.io-index)",
+]
+
+[[package]]
+name = "phf_generator"
+version = "0.7.24"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+dependencies = [
+ "phf_shared 0.7.24 (registry+https://github.com/rust-lang/crates.io-index)",
+ "rand 0.6.5 (registry+https://github.com/rust-lang/crates.io-index)",
+]
+
+[[package]]
+name = "phf_shared"
+version = "0.7.24"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+dependencies = [
+ "siphasher 0.2.3 (registry+https://github.com/rust-lang/crates.io-index)",
+]
+
+[[package]]
+name = "pkg-config"
+version = "0.3.14"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+
+[[package]]
+name = "pnacl-build-helper"
+version = "1.4.11"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+dependencies = [
+ "tempdir 0.3.7 (registry+https://github.com/rust-lang/crates.io-index)",
+ "walkdir 1.0.7 (registry+https://github.com/rust-lang/crates.io-index)",
+]
+
+[[package]]
+name = "precomputed-hash"
+version = "0.1.1"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+
+[[package]]
+name = "proc-macro2"
+version = "0.4.30"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+dependencies = [
+ "unicode-xid 0.1.0 (registry+https://github.com/rust-lang/crates.io-index)",
+]
+
+[[package]]
+name = "quote"
+version = "0.6.12"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+dependencies = [
+ "proc-macro2 0.4.30 (registry+https://github.com/rust-lang/crates.io-index)",
+]
+
+[[package]]
+name = "rand"
+version = "0.4.6"
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new file mode 100644
index 000000000000..ce297a6a0515
--- /dev/null
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+                "sha256:8f9a95b66969cdea53ec992ecea5406c5bd99c9221f539bca1e8406b200ae98c",
+                "sha256:932c03d2d565f75961ba1d3cec41ddde00e162c5b46d03f7423edcb807734eab",
+                "sha256:988529edadc49039d205e0aa6ce049c5ccda4acb2d6c3c5c550c17e8c02c05ba",
+                "sha256:998d7e73548fe395eeb294495a04d38942edb66d1fa61eb70418871bc621227e",
+                "sha256:9de60893fb447d1e797f6bf08fdf0dbcda0c1e34c1b06c92bd3a363c0ea8c609",
+                "sha256:9e80d45d0c7fcee54e22771db7f1b0b126fb4a6c0a2e5afa72f66827207ff2f2",
+                "sha256:a545a3dfe5082dc8e8c3eb7f8a2cf4f2870902ff1860bd99b6198cfd1f9d1f49",
+                "sha256:a5d8f29e5ec661143621a8f4de51adfb300d7a476224156a39a392254f70687b",
+                "sha256:aca06bfba4759bbdb09bf52ebb15ae20268ee1f6747417837926fae990ebc41d",
+                "sha256:bb23b7a6fd666e551a3094ab896a57809e010059540ad20acbeec03a154224ce",
+                "sha256:bfd1d0ae7e292105f29d7deaa9d8f2916ed8553ab9d5f39ec65bcf5deadff3f9",
+                "sha256:c62ca0a38958f541a73cf86acdab020c2091631c137bd359c4f5bddde7b75fd4",
+                "sha256:c709d8bda72cf4cd348ccec2a4881f2c5848fd72903c185f363d361b2737f773",
+                "sha256:c968a6aa7e0b56ecbd28531ddf439c2ec103610d3e2bf3b75b813304f8cb7723",
+                "sha256:df785d8cb80539d0b55fd47183264b7002077859028dfe3070cf6359bf8b2d9c",
+                "sha256:f406628ca51e0ae90ae76ea8398677a921b36f0bd71aab2099dfed08abd0322f",
+                "sha256:f46087bbd95ebae244a0eda01a618aff11ec7a069b15a3ef8f6b520db523dcf1",
+                "sha256:f8019c5279eb32360ca03e9fac40a12667715546eed5c5eb59eb381f2f501260",
+                "sha256:fc5f4d209733750afd2714e9109816a29500718b32dd9a5db01c0cb3a019b96a"
+            ],
+            "index": "pypi",
+            "version": "==4.5.3"
+        },
+        "dredd-hooks": {
+            "hashes": [
+                "sha256:7d0527ee269d716126de912098b6d8750fcb3755232cb902e5a360f1921df780"
+            ],
+            "index": "pypi",
+            "version": "==0.2.0"
+        },
+        "entrypoints": {
+            "hashes": [
+                "sha256:589f874b313739ad35be6e0cd7efde2a4e9b6fea91edcc34e58ecbb8dbe56d19",
+                "sha256:c70dd71abe5a8c85e55e12c19bd91ccfeec11a6e99044204511f9ed547d48451"
+            ],
+            "version": "==0.3"
+        },
+        "factory-boy": {
+            "hashes": [
+                "sha256:6f25cc4761ac109efd503f096e2ad99421b1159f01a29dbb917359dcd68e08ca",
+                "sha256:d552cb872b310ae78bd7429bf318e42e1e903b1a109e899a523293dfa762ea4f"
+            ],
+            "index": "pypi",
+            "version": "==2.11.1"
+        },
+        "faker": {
+            "hashes": [
+                "sha256:00b7011757c4907546f17d0e47df098b542ea2b04c966ee0e80a493aae2c13c8",
+                "sha256:745ac8b9c9526e338696e07b7f2e206e5e317e5744e22fdd7c2894bf19af41f1"
+            ],
+            "version": "==1.0.4"
+        },
+        "flake8": {
+            "hashes": [
+                "sha256:859996073f341f2670741b51ec1e67a01da142831aa1fdc6242dbf88dffbe661",
+                "sha256:a796a115208f5c03b18f332f7c11729812c8c3ded6c46319c59b53efd3819da8"
+            ],
+            "index": "pypi",
+            "version": "==3.7.7"
+        },
+        "identify": {
+            "hashes": [
+                "sha256:244e7864ef59f0c7c50c6db73f58564151d91345cd9b76ed793458953578cadd",
+                "sha256:8ff062f90ad4b09cfe79b5dfb7a12e40f19d2e68a5c9598a49be45f16aba7171"
+            ],
+            "version": "==1.4.1"
+        },
+        "importlib-metadata": {
+            "hashes": [
+                "sha256:46fc60c34b6ed7547e2a723fc8de6dc2e3a1173f8423246b3ce497f064e9c3de",
+                "sha256:bc136180e961875af88b1ab85b4009f4f1278f8396a60526c0009f503a1a96ca"
+            ],
+            "version": "==0.9"
+        },
+        "isort": {
+            "hashes": [
+                "sha256:01cb7e1ca5e6c5b3f235f0385057f70558b70d2f00320208825fa62887292f43",
+                "sha256:268067462aed7eb2a1e237fcb287852f22077de3fb07964e87e00f829eea2d1a"
+            ],
+            "index": "pypi",
+            "version": "==4.3.17"
+        },
+        "mccabe": {
+            "hashes": [
+                "sha256:ab8a6258860da4b6677da4bd2fe5dc2c659cff31b3ee4f7f5d64e79735b80d42",
+                "sha256:dd8d182285a0fe56bace7f45b5e7d1a6ebcbf524e8f3bd87eb0f125271b8831f"
+            ],
+            "version": "==0.6.1"
+        },
+        "more-itertools": {
+            "hashes": [
+                "sha256:2112d2ca570bb7c3e53ea1a35cd5df42bb0fd10c45f0fb97178679c3c03d64c7",
+                "sha256:c3e4748ba1aad8dba30a4886b0b1a2004f9a863837b8654e7059eebf727afa5a"
+            ],
+            "index": "pypi",
+            "version": "==7.0.0"
+        },
+        "nodeenv": {
+            "hashes": [
+                "sha256:ad8259494cf1c9034539f6cced78a1da4840a4b157e23640bc4a0c0546b0cb7a"
+            ],
+            "version": "==1.3.3"
+        },
+        "numpy": {
+            "hashes": [
+                "sha256:1980f8d84548d74921685f68096911585fee393975f53797614b34d4f409b6da",
+                "sha256:22752cd809272671b273bb86df0f505f505a12368a3a5fc0aa811c7ece4dfd5c",
+                "sha256:23cc40313036cffd5d1873ef3ce2e949bdee0646c5d6f375bf7ee4f368db2511",
+                "sha256:2b0b118ff547fecabc247a2668f48f48b3b1f7d63676ebc5be7352a5fd9e85a5",
+                "sha256:3a0bd1edf64f6a911427b608a894111f9fcdb25284f724016f34a84c9a3a6ea9",
+                "sha256:3f25f6c7b0d000017e5ac55977a3999b0b1a74491eacb3c1aa716f0e01f6dcd1",
+                "sha256:4061c79ac2230594a7419151028e808239450e676c39e58302ad296232e3c2e8",
+                "sha256:560ceaa24f971ab37dede7ba030fc5d8fa173305d94365f814d9523ffd5d5916",
+                "sha256:62be044cd58da2a947b7e7b2252a10b42920df9520fc3d39f5c4c70d5460b8ba",
+                "sha256:6c692e3879dde0b67a9dc78f9bfb6f61c666b4562fd8619632d7043fb5b691b0",
+                "sha256:6f65e37b5a331df950ef6ff03bd4136b3c0bbcf44d4b8e99135d68a537711b5a",
+                "sha256:7a78cc4ddb253a55971115f8320a7ce28fd23a065fc33166d601f51760eecfa9",
+                "sha256:80a41edf64a3626e729a62df7dd278474fc1726836552b67a8c6396fd7e86760",
+                "sha256:893f4d75255f25a7b8516feb5766c6b63c54780323b9bd4bc51cdd7efc943c73",
+                "sha256:972ea92f9c1b54cc1c1a3d8508e326c0114aaf0f34996772a30f3f52b73b942f",
+                "sha256:9f1d4865436f794accdabadc57a8395bd3faa755449b4f65b88b7df65ae05f89",
+                "sha256:9f4cd7832b35e736b739be03b55875706c8c3e5fe334a06210f1a61e5c2c8ca5",
+                "sha256:adab43bf657488300d3aeeb8030d7f024fcc86e3a9b8848741ea2ea903e56610",
+                "sha256:bd2834d496ba9b1bdda3a6cf3de4dc0d4a0e7be306335940402ec95132ad063d",
+                "sha256:d20c0360940f30003a23c0adae2fe50a0a04f3e48dc05c298493b51fd6280197",
+                "sha256:d3b3ed87061d2314ff3659bb73896e622252da52558f2380f12c421fbdee3d89",
+                "sha256:dc235bf29a406dfda5790d01b998a1c01d7d37f449128c0b1b7d1c89a84fae8b",
+                "sha256:fb3c83554f39f48f3fa3123b9c24aecf681b1c289f9334f8215c1d3c8e2f6e5b"
+            ],
+            "version": "==1.16.2"
+        },
+        "pandas": {
+            "hashes": [
+                "sha256:071e42b89b57baa17031af8c6b6bbd2e9a5c68c595bc6bf9adabd7a9ed125d3b",
+                "sha256:17450e25ae69e2e6b303817bdf26b2cd57f69595d8550a77c308be0cd0fd58fa",
+                "sha256:17916d818592c9ec891cbef2e90f98cc85e0f1e89ed0924c9b5220dc3209c846",
+                "sha256:2538f099ab0e9f9c9d09bbcd94b47fd889bad06dc7ae96b1ed583f1dc1a7a822",
+                "sha256:366f30710172cb45a6b4f43b66c220653b1ea50303fbbd94e50571637ffb9167",
+                "sha256:42e5ad741a0d09232efbc7fc648226ed93306551772fc8aecc6dce9f0e676794",
+                "sha256:4e718e7f395ba5bfe8b6f6aaf2ff1c65a09bb77a36af6394621434e7cc813204",
+                "sha256:4f919f409c433577a501e023943e582c57355d50a724c589e78bc1d551a535a2",
+                "sha256:4fe0d7e6438212e839fc5010c78b822664f1a824c0d263fd858f44131d9166e2",
+                "sha256:5149a6db3e74f23dc3f5a216c2c9ae2e12920aa2d4a5b77e44e5b804a5f93248",
+                "sha256:627594338d6dd995cfc0bacd8e654cd9e1252d2a7c959449228df6740d737eb8",
+                "sha256:83c702615052f2a0a7fb1dd289726e29ec87a27272d775cb77affe749cca28f8",
+                "sha256:8c872f7fdf3018b7891e1e3e86c55b190e6c5cee70cab771e8f246c855001296",
+                "sha256:90f116086063934afd51e61a802a943826d2aac572b2f7d55caaac51c13db5b5",
+                "sha256:a3352bacac12e1fc646213b998bce586f965c9d431773d9e91db27c7c48a1f7d",
+                "sha256:bcdd06007cca02d51350f96debe51331dec429ac8f93930a43eb8fb5639e3eb5",
+                "sha256:c1bd07ebc15285535f61ddd8c0c75d0d6293e80e1ee6d9a8d73f3f36954342d0",
+                "sha256:c9a4b7c55115eb278c19aa14b34fcf5920c8fe7797a09b7b053ddd6195ea89b3",
+                "sha256:cc8fc0c7a8d5951dc738f1c1447f71c43734244453616f32b8aa0ef6013a5dfb",
+                "sha256:d7b460bc316064540ce0c41c1438c416a40746fd8a4fb2999668bf18f3c4acf1"
+            ],
+            "index": "pypi",
+            "version": "==0.24.2"
+        },
+        "pre-commit": {
+            "hashes": [
+                "sha256:75a9110eae00d009c913616c0fc8a6a02e7716c4a29a14cac9b313d2c7338ab0",
+                "sha256:f882c65316eb5b705fe4613e92a7c91055c1800102e4d291cfd18912ec9cf90e"
+            ],
+            "index": "pypi",
+            "version": "==1.15.1"
+        },
+        "pycodestyle": {
+            "hashes": [
+                "sha256:95a2219d12372f05704562a14ec30bc76b05a5b297b21a5dfe3f6fac3491ae56",
+                "sha256:e40a936c9a450ad81df37f549d676d127b1b66000a6c500caa2b085bc0ca976c"
+            ],
+            "version": "==2.5.0"
+        },
+        "pydot": {
+            "hashes": [
+                "sha256:67be714300c78fda5fd52f79ec994039e3f76f074948c67b5ff539b433ad354f",
+                "sha256:d49c9d4dd1913beec2a997f831543c8cbd53e535b1a739e921642fe416235f01"
+            ],
+            "index": "pypi",
+            "version": "==1.4.1"
+        },
+        "pyflakes": {
+            "hashes": [
+                "sha256:17dbeb2e3f4d772725c777fabc446d5634d1038f234e77343108ce445ea69ce0",
+                "sha256:d976835886f8c5b31d47970ed689944a0262b5f3afa00a5a7b4dc81e5449f8a2"
+            ],
+            "version": "==2.1.1"
+        },
+        "pyparsing": {
+            "hashes": [
+                "sha256:1873c03321fc118f4e9746baf201ff990ceb915f433f23b395f5580d1840cb2a",
+                "sha256:9b6323ef4ab914af344ba97510e966d64ba91055d6b9afa6b30799340e89cc03"
+            ],
+            "index": "pypi",
+            "version": "==2.4.0"
+        },
+        "python-dateutil": {
+            "hashes": [
+                "sha256:7e6584c74aeed623791615e26efd690f29817a27c73085b78e4bad02493df2fb",
+                "sha256:c89805f6f4d64db21ed966fda138f8a5ed7a4fdbc1a8ee329ce1b74e3c74da9e"
+            ],
+            "markers": "python_version >= '2.7'",
+            "version": "==2.8.0"
+        },
+        "pytz": {
+            "hashes": [
+                "sha256:303879e36b721603cc54604edcac9d20401bdbe31e1e4fdee5b9f98d5d31dfda",
+                "sha256:d747dd3d23d77ef44c6a3526e274af6efeb0a6f1afd5a69ba4d5be4098c8e141"
+            ],
+            "version": "==2019.1"
+        },
+        "pyyaml": {
+            "hashes": [
+                "sha256:1adecc22f88d38052fb787d959f003811ca858b799590a5eaa70e63dca50308c",
+                "sha256:436bc774ecf7c103814098159fbb84c2715d25980175292c648f2da143909f95",
+                "sha256:460a5a4248763f6f37ea225d19d5c205677d8d525f6a83357ca622ed541830c2",
+                "sha256:5a22a9c84653debfbf198d02fe592c176ea548cccce47553f35f466e15cf2fd4",
+                "sha256:7a5d3f26b89d688db27822343dfa25c599627bc92093e788956372285c6298ad",
+                "sha256:9372b04a02080752d9e6f990179a4ab840227c6e2ce15b95e1278456664cf2ba",
+                "sha256:a5dcbebee834eaddf3fa7366316b880ff4062e4bcc9787b78c7fbb4a26ff2dd1",
+                "sha256:aee5bab92a176e7cd034e57f46e9df9a9862a71f8f37cad167c6fc74c65f5b4e",
+                "sha256:c51f642898c0bacd335fc119da60baae0824f2cde95b0330b56c0553439f0673",
+                "sha256:c68ea4d3ba1705da1e0d85da6684ac657912679a649e8868bd850d2c299cce13",
+                "sha256:e23d0cc5299223dcc37885dae624f382297717e459ea24053709675a976a3e19"
+            ],
+            "index": "pypi",
+            "version": "==5.1"
+        },
+        "selenium": {
+            "hashes": [
+                "sha256:2d7131d7bc5a5b99a2d9b04aaf2612c411b03b8ca1b1ee8d3de5845a9be2cb3c",
+                "sha256:deaf32b60ad91a4611b98d8002757f29e6f2c2d5fcaf202e1c9ad06d6772300d"
+            ],
+            "index": "pypi",
+            "version": "==3.141.0"
+        },
+        "six": {
+            "hashes": [
+                "sha256:3350809f0555b11f552448330d0b52d5f24c91a322ea4a15ef22629740f3761c",
+                "sha256:d16a0141ec1a18405cd4ce8b4613101da75da0e9a7aec5bdd4fa804d0e0eba73"
+            ],
+            "version": "==1.12.0"
+        },
+        "tblib": {
+            "hashes": [
+                "sha256:436e4200e63d92316551179dc540906652878df4ff39b43db30fcf6400444fe7",
+                "sha256:9bae4b8c44b06af0e114bfc4d5f6aa3eafd2119af5a4dcab34f51f1665f16c59"
+            ],
+            "index": "pypi",
+            "version": "==1.3.2"
+        },
+        "text-unidecode": {
+            "hashes": [
+                "sha256:5a1375bb2ba7968740508ae38d92e1f889a0832913cb1c447d5e2046061a396d",
+                "sha256:801e38bd550b943563660a91de8d4b6fa5df60a542be9093f7abf819f86050cc"
+            ],
+            "version": "==1.2"
+        },
+        "toml": {
+            "hashes": [
+                "sha256:229f81c57791a41d65e399fc06bf0848bab550a9dfd5ed66df18ce5f05e73d5c",
+                "sha256:235682dd292d5899d361a811df37e04a8828a5b1da3115886b73cf81ebc9100e"
+            ],
+            "version": "==0.10.0"
+        },
+        "urllib3": {
+            "hashes": [
+                "sha256:61bf29cada3fc2fbefad4fdf059ea4bd1b4a86d2b6d15e1c7c0b582b9752fe39",
+                "sha256:de9529817c93f27c8ccbfead6985011db27bd0ddfcdb2d86f3f663385c6a9c22"
+            ],
+            "markers": "python_version >= '3.4'",
+            "version": "==1.24.1"
+        },
+        "virtualenv": {
+            "hashes": [
+                "sha256:6aebaf4dd2568a0094225ebbca987859e369e3e5c22dc7d52e5406d504890417",
+                "sha256:984d7e607b0a5d1329425dd8845bd971b957424b5ba664729fab51ab8c11bc39"
+            ],
+            "version": "==16.4.3"
+        },
+        "zipp": {
+            "hashes": [
+                "sha256:55ca87266c38af6658b84db8cfb7343cdb0bf275f93c7afaea0d8e7a209c7478",
+                "sha256:682b3e1c62b7026afe24eadf6be579fb45fec54c07ea218bded8092af07a68c4"
+            ],
+            "version": "==0.3.3"
+        }
+    }
+}
diff --git a/integration/testdata/test-repo.json.golden b/integration/testdata/test-repo.json.golden
index 360ba1f3f097..07cb12e69eef 100644
--- a/integration/testdata/test-repo.json.golden
+++ b/integration/testdata/test-repo.json.golden
@@ -1,7 +1,7 @@
 {
   "SchemaVersion": 2,
   "CreatedAt": "2021-08-25T12:20:30.000000005Z",
-  "ArtifactName": "https://github.com/knqyf263/trivy-ci-test",
+  "ArtifactName": "testdata/fixtures/repo/trivy-ci-test",
   "ArtifactType": "repository",
   "Metadata": {
     "ImageConfig": {
@@ -109,6 +109,11 @@
           "LastModifiedDate": "2021-08-16T16:37:00Z"
         }
       ]
+    },
+    {
+      "Target": "Pipfile.lock",
+      "Class": "lang-pkgs",
+      "Type": "pipenv"
     }
   ]
 }
diff --git a/pkg/commands/app_test.go b/pkg/commands/app_test.go
index 858e2ed6b245..143de739caf0 100644
--- a/pkg/commands/app_test.go
+++ b/pkg/commands/app_test.go
@@ -197,6 +197,7 @@ func TestFlags(t *testing.T) {
 				scanners: types.Scanners{
 					types.VulnerabilityScanner,
 					types.SecretScanner,
+					types.SBOMScanner,
 				},
 			},
 		},
@@ -216,6 +217,7 @@ func TestFlags(t *testing.T) {
 				scanners: types.Scanners{
 					types.VulnerabilityScanner,
 					types.SecretScanner,
+					types.SBOMScanner,
 				},
 			},
 		},
@@ -237,6 +239,7 @@ func TestFlags(t *testing.T) {
 				scanners: types.Scanners{
 					types.VulnerabilityScanner,
 					types.SecretScanner,
+					types.SBOMScanner,
 				},
 			},
 		},
@@ -257,6 +260,7 @@ func TestFlags(t *testing.T) {
 				scanners: types.Scanners{
 					types.VulnerabilityScanner,
 					types.SecretScanner,
+					types.SBOMScanner,
 				},
 			},
 		},
diff --git a/pkg/commands/artifact/run.go b/pkg/commands/artifact/run.go
index f61e84928265..afdbf2ee6966 100644
--- a/pkg/commands/artifact/run.go
+++ b/pkg/commands/artifact/run.go
@@ -538,7 +538,6 @@ func initScannerConfig(opts flag.Options, cacheClient cache.Cache) (ScannerConfi
 		Scanners:            opts.Scanners,
 		ImageConfigScanners: opts.ImageConfigScanners, // this is valid only for 'image' subcommand
 		ScanRemovedPackages: opts.ScanRemovedPkgs,     // this is valid only for 'image' subcommand
-		ListAllPackages:     opts.ListAllPkgs,
 		LicenseCategories:   opts.LicenseCategories,
 		FilePatterns:        opts.FilePatterns,
 		IncludeDevDeps:      opts.IncludeDevDeps,
diff --git a/pkg/flag/options.go b/pkg/flag/options.go
index 9f4032fb9711..13ed256b1c35 100644
--- a/pkg/flag/options.go
+++ b/pkg/flag/options.go
@@ -354,16 +354,7 @@ type Options struct {
 
 // Align takes consistency of options
 func (o *Options) Align() error {
-	if o.Format == types.FormatSPDX || o.Format == types.FormatSPDXJSON {
-		log.Info(`"--format spdx" and "--format spdx-json" disable security scanning`)
-		o.Scanners = nil
-	}
-
-	// Vulnerability scanning is disabled by default for CycloneDX.
-	if o.Format == types.FormatCycloneDX && !viper.IsSet(ScannersFlag.ConfigName) {
-		log.Info(`"--format cyclonedx" disables security scanning. Specify "--scanners vuln" explicitly if you want to include vulnerabilities in the CycloneDX report.`)
-		o.Scanners = nil
-	}
+	o.enableSBOM()
 
 	if o.Compliance.Spec.ID != "" {
 		if viper.IsSet(ScannersFlag.ConfigName) {
@@ -394,6 +385,32 @@ func (o *Options) Align() error {
 	return nil
 }
 
+func (o *Options) enableSBOM() {
+	// Always need packages when the vulnerability scanner is enabled
+	if o.Scanners.Enabled(types.VulnerabilityScanner) {
+		o.Scanners.Enable(types.SBOMScanner)
+	}
+
+	// Enable the SBOM scanner when a list of packages is necessary.
+	if o.ListAllPkgs || slices.Contains(types.SupportedSBOMFormats, o.Format) {
+		o.Scanners.Enable(types.SBOMScanner)
+	}
+
+	if o.Format == types.FormatSPDX || o.Format == types.FormatSPDXJSON {
+		log.Info(`"--format spdx" and "--format spdx-json" disable security scanning`)
+		o.Scanners = types.Scanners{types.SBOMScanner}
+	}
+
+	if o.Format == types.FormatCycloneDX {
+		// Vulnerability scanning is disabled by default for CycloneDX.
+		if !viper.IsSet(ScannersFlag.ConfigName) {
+			log.Info(`"--format cyclonedx" disables security scanning. Specify "--scanners vuln" explicitly if you want to include vulnerabilities in the CycloneDX report.`)
+			o.Scanners = nil
+		}
+		o.Scanners.Enable(types.SBOMScanner)
+	}
+}
+
 // RegistryOpts returns options for OCI registries
 func (o *Options) RegistryOpts() ftypes.RegistryOptions {
 	return ftypes.RegistryOptions{
diff --git a/pkg/flag/report_flags.go b/pkg/flag/report_flags.go
index 852710248972..d359f1f1b5b6 100644
--- a/pkg/flag/report_flags.go
+++ b/pkg/flag/report_flags.go
@@ -54,7 +54,7 @@ var (
 	ListAllPkgsFlag = Flag[bool]{
 		Name:       "list-all-pkgs",
 		ConfigName: "list-all-pkgs",
-		Usage:      "enabling the option will output all packages regardless of vulnerability",
+		Usage:      "output all packages in the JSON report regardless of vulnerability",
 	}
 	IgnoreFileFlag = Flag[string]{
 		Name:       "ignorefile",
@@ -208,10 +208,10 @@ func (f *ReportFlagGroup) ToOptions() (ReportOptions, error) {
 		}
 	}
 
-	// "--list-all-pkgs" option is unavailable with "--format table".
-	// If user specifies "--list-all-pkgs" with "--format table", we should warn it.
-	if listAllPkgs && format == types.FormatTable {
-		log.Warn(`"--list-all-pkgs" cannot be used with "--format table". Try "--format json" or other formats.`)
+	// "--list-all-pkgs" option is unavailable with other than "--format json".
+	// If user specifies "--list-all-pkgs" with "--format table" or other formats, we should warn it.
+	if listAllPkgs && format != types.FormatJSON {
+		log.Warn(`"--list-all-pkgs" is only valid for the JSON format, for other formats a list of packages is automatically included.`)
 	}
 
 	// "--dependency-tree" option is available only with "--format table".
@@ -224,11 +224,6 @@ func (f *ReportFlagGroup) ToOptions() (ReportOptions, error) {
 		}
 	}
 
-	// Enable '--list-all-pkgs' if needed
-	if f.forceListAllPkgs(format, listAllPkgs, dependencyTree) {
-		listAllPkgs = true
-	}
-
 	cs, err := loadComplianceTypes(f.Compliance.Value())
 	if err != nil {
 		return ReportOptions{}, xerrors.Errorf("unable to load compliance spec: %w", err)
@@ -273,23 +268,6 @@ func loadComplianceTypes(compliance string) (spec.ComplianceSpec, error) {
 	return cs, nil
 }
 
-func (f *ReportFlagGroup) forceListAllPkgs(format types.Format, listAllPkgs, dependencyTree bool) bool {
-	if slices.Contains(types.SupportedSBOMFormats, format) && !listAllPkgs {
-		log.Debugf("%q automatically enables '--list-all-pkgs'.", types.SupportedSBOMFormats)
-		return true
-	}
-	// We need this flag to insert dependency locations into Sarif('Package' struct contains 'Locations')
-	if format == types.FormatSarif && !listAllPkgs {
-		log.Debug("Sarif format automatically enables '--list-all-pkgs' to get locations")
-		return true
-	}
-	if dependencyTree && !listAllPkgs {
-		log.Debug("'--dependency-tree' enables '--list-all-pkgs'.")
-		return true
-	}
-	return false
-}
-
 func toSeverity(severity []string) []dbTypes.Severity {
 	if len(severity) == 0 {
 		return nil
diff --git a/pkg/flag/report_flags_test.go b/pkg/flag/report_flags_test.go
index 58b050fd095b..6e56904c4dcf 100644
--- a/pkg/flag/report_flags_test.go
+++ b/pkg/flag/report_flags_test.go
@@ -46,34 +46,12 @@ func TestReportFlagGroup_ToOptions(t *testing.T) {
 		{
 			name: "happy path with an cyclonedx",
 			fields: fields{
-				severities:  "CRITICAL",
-				format:      "cyclonedx",
-				listAllPkgs: true,
-			},
-			want: flag.ReportOptions{
-				Severities:  []dbTypes.Severity{dbTypes.SeverityCritical},
-				Format:      types.FormatCycloneDX,
-				ListAllPkgs: true,
-			},
-		},
-		{
-			name: "happy path with an cyclonedx option list-all-pkgs is false",
-			fields: fields{
-				severities:  "CRITICAL",
-				format:      "cyclonedx",
-				listAllPkgs: false,
-				debug:       true,
-			},
-			wantLogs: []string{
-				`["cyclonedx" "spdx" "spdx-json" "github"] automatically enables '--list-all-pkgs'.`,
-				`Parsed severities	severities=[CRITICAL]`,
+				severities: "CRITICAL",
+				format:     "cyclonedx",
 			},
 			want: flag.ReportOptions{
-				Severities: []dbTypes.Severity{
-					dbTypes.SeverityCritical,
-				},
-				Format:      types.FormatCycloneDX,
-				ListAllPkgs: true,
+				Severities: []dbTypes.Severity{dbTypes.SeverityCritical},
+				Format:     types.FormatCycloneDX,
 			},
 		},
 		{
@@ -128,7 +106,7 @@ func TestReportFlagGroup_ToOptions(t *testing.T) {
 				listAllPkgs: true,
 			},
 			wantLogs: []string{
-				`"--list-all-pkgs" cannot be used with "--format table". Try "--format json" or other formats.`,
+				`"--list-all-pkgs" is only valid for the JSON format, for other formats a list of packages is automatically included.`,
 			},
 			want: flag.ReportOptions{
 				Format:      "table",
@@ -224,7 +202,7 @@ func TestReportFlagGroup_ToOptions(t *testing.T) {
 
 			got, err := f.ToOptions()
 			require.NoError(t, err)
-			assert.Equalf(t, tt.want, got, "ToOptions()")
+			assert.EqualExportedValuesf(t, tt.want, got, "ToOptions()")
 
 			// Assert log messages
 			assert.Equal(t, tt.wantLogs, out.Messages(), tt.name)
diff --git a/pkg/report/json.go b/pkg/report/json.go
index 57ac92cfe8ca..8529b5274560 100644
--- a/pkg/report/json.go
+++ b/pkg/report/json.go
@@ -6,6 +6,7 @@ import (
 	"fmt"
 	"io"
 
+	"github.com/samber/lo"
 	"golang.org/x/xerrors"
 
 	"github.com/aquasecurity/trivy/pkg/types"
@@ -13,11 +14,22 @@ import (
 
 // JSONWriter implements result Writer
 type JSONWriter struct {
-	Output io.Writer
+	Output      io.Writer
+	ListAllPkgs bool
 }
 
 // Write writes the results in JSON format
-func (jw JSONWriter) Write(ctx context.Context, report types.Report) error {
+func (jw JSONWriter) Write(_ context.Context, report types.Report) error {
+	if !jw.ListAllPkgs {
+		// Delete packages
+		for i := range report.Results {
+			report.Results[i].Packages = nil
+		}
+	}
+	report.Results = lo.Filter(report.Results, func(r types.Result, _ int) bool {
+		return r.Target != "" || !r.IsEmpty()
+	})
+
 	output, err := json.MarshalIndent(report, "", "  ")
 	if err != nil {
 		return xerrors.Errorf("failed to marshal json: %w", err)
diff --git a/pkg/report/writer.go b/pkg/report/writer.go
index b4966d88a700..041c9acdfe8e 100644
--- a/pkg/report/writer.go
+++ b/pkg/report/writer.go
@@ -55,7 +55,10 @@ func Write(ctx context.Context, report types.Report, option flag.Options) (err e
 			IgnoredLicenses:      option.IgnoredLicenses,
 		}
 	case types.FormatJSON:
-		writer = &JSONWriter{Output: output}
+		writer = &JSONWriter{
+			Output:      output,
+			ListAllPkgs: option.ListAllPkgs,
+		}
 	case types.FormatGitHub:
 		writer = &github.Writer{
 			Output:  output,
@@ -76,7 +79,6 @@ func Write(ctx context.Context, report types.Report, option flag.Options) (err e
 			}
 			break
 		}
-		var err error
 		if writer, err = NewTemplateWriter(output, option.Template, option.AppVersion); err != nil {
 			return xerrors.Errorf("failed to initialize template writer: %w", err)
 		}
diff --git a/pkg/rpc/client/client.go b/pkg/rpc/client/client.go
index 36a69b88c04f..c2bcae2793a4 100644
--- a/pkg/rpc/client/client.go
+++ b/pkg/rpc/client/client.go
@@ -84,7 +84,6 @@ func (s Scanner) Scan(ctx context.Context, target, artifactKey string, blobKeys
 			Options: &rpc.ScanOptions{
 				VulnType:          opts.VulnType,
 				Scanners:          xstrings.ToStringSlice(opts.Scanners),
-				ListAllPackages:   opts.ListAllPackages,
 				LicenseCategories: licenseCategories,
 				IncludeDevDeps:    opts.IncludeDevDeps,
 			},
diff --git a/pkg/rpc/server/server.go b/pkg/rpc/server/server.go
index 5d9bc426703f..79801b3bd212 100644
--- a/pkg/rpc/server/server.go
+++ b/pkg/rpc/server/server.go
@@ -47,10 +47,9 @@ func (s *ScanServer) Scan(ctx context.Context, in *rpcScanner.ScanRequest) (*rpc
 		return types.Scanner(s)
 	})
 	options := types.ScanOptions{
-		VulnType:        in.Options.VulnType,
-		Scanners:        scanners,
-		ListAllPackages: in.Options.ListAllPackages,
-		IncludeDevDeps:  in.Options.IncludeDevDeps,
+		VulnType:       in.Options.VulnType,
+		Scanners:       scanners,
+		IncludeDevDeps: in.Options.IncludeDevDeps,
 	}
 	results, os, err := s.localScanner.Scan(ctx, in.Target, in.ArtifactId, in.BlobIds, options)
 	if err != nil {
diff --git a/pkg/scanner/langpkg/scan.go b/pkg/scanner/langpkg/scan.go
index 6fb394d31336..d3923033e3f0 100644
--- a/pkg/scanner/langpkg/scan.go
+++ b/pkg/scanner/langpkg/scan.go
@@ -54,10 +54,8 @@ func (s *scanner) Scan(ctx context.Context, target types.ScanTarget, opts types.
 			Type:   app.Type,
 		}
 
-		if opts.ListAllPackages {
-			sort.Sort(app.Packages)
-			result.Packages = app.Packages
-		}
+		sort.Sort(app.Packages)
+		result.Packages = app.Packages
 
 		if opts.Scanners.Enabled(types.VulnerabilityScanner) {
 			var err error
diff --git a/pkg/scanner/local/scan.go b/pkg/scanner/local/scan.go
index 99146de0d55b..9a73ad97dbfa 100644
--- a/pkg/scanner/local/scan.go
+++ b/pkg/scanner/local/scan.go
@@ -153,7 +153,7 @@ func (s Scanner) ScanTarget(ctx context.Context, target types.ScanTarget, option
 
 func (s Scanner) scanVulnerabilities(ctx context.Context, target types.ScanTarget, options types.ScanOptions) (
 	types.Results, bool, error) {
-	if !options.ListAllPackages && !options.Scanners.Enabled(types.VulnerabilityScanner) {
+	if !options.Scanners.AnyEnabled(types.SBOMScanner, types.VulnerabilityScanner) {
 		return nil, false, nil
 	}
 
diff --git a/pkg/scanner/local/scan_test.go b/pkg/scanner/local/scan_test.go
index 9bc8124d10ee..42a189ba5d68 100644
--- a/pkg/scanner/local/scan_test.go
+++ b/pkg/scanner/local/scan_test.go
@@ -21,6 +21,58 @@ import (
 	"github.com/aquasecurity/trivy/pkg/vulnerability"
 )
 
+var (
+	muslPkg = ftypes.Package{
+		Name:       "musl",
+		Version:    "1.2.3",
+		SrcName:    "musl",
+		SrcVersion: "1.2.3",
+		Licenses:   []string{"MIT"},
+		Layer: ftypes.Layer{
+			DiffID: "sha256:ebf12965380b39889c99a9c02e82ba465f887b45975b6e389d42e9e6a3857888",
+		},
+	}
+	railsPkg = ftypes.Package{
+		Name:    "rails",
+		Version: "4.0.2",
+		Layer: ftypes.Layer{
+			DiffID: "sha256:0ea33a93585cf1917ba522b2304634c3073654062d5282c1346322967790ef33",
+		},
+	}
+	innocentPkg = ftypes.Package{
+		Name:    "innocent",
+		Version: "1.2.3",
+		Layer: ftypes.Layer{
+			DiffID: "sha256:0ea33a93585cf1917ba522b2304634c3073654062d5282c1346322967790ef33",
+		},
+	}
+	uuidPkg = ftypes.Package{
+		Name:     "github.com/google/uuid",
+		Version:  "1.6.0",
+		FilePath: "",
+		Layer: ftypes.Layer{
+			DiffID: "sha256:0ea33a93585cf1917ba522b2304634c3073654062d5282c1346322967790ef33",
+		},
+		Licenses: []string{"LGPL"},
+	}
+	urllib3Pkg = ftypes.Package{
+		Name:     "urllib3",
+		Version:  "3.2.1",
+		FilePath: "/usr/lib/python/site-packages/urllib3-3.2.1/METADATA",
+		Layer: ftypes.Layer{
+			DiffID: "sha256:0ea33a93585cf1917ba522b2304634c3073654062d5282c1346322967790ef33",
+		},
+		Licenses: []string{"MIT"},
+	}
+	laravelPkg = ftypes.Package{
+		Name:    "laravel/framework",
+		Version: "6.0.0",
+		Layer: ftypes.Layer{
+			DiffID: "sha256:0ea33a93585cf1917ba522b2304634c3073654062d5282c1346322967790ef33",
+		},
+	}
+)
+
 func TestScanner_Scan(t *testing.T) {
 	type args struct {
 		target   string
@@ -61,28 +113,14 @@ func TestScanner_Scan(t *testing.T) {
 							Name:   "3.11",
 						},
 						Packages: []ftypes.Package{
-							{
-								Name:       "musl",
-								Version:    "1.2.3",
-								SrcName:    "musl",
-								SrcVersion: "1.2.3",
-								Layer: ftypes.Layer{
-									DiffID: "sha256:ebf12965380b39889c99a9c02e82ba465f887b45975b6e389d42e9e6a3857888",
-								},
-							},
+							muslPkg,
 						},
 						Applications: []ftypes.Application{
 							{
 								Type:     ftypes.Bundler,
 								FilePath: "/app/Gemfile.lock",
 								Packages: []ftypes.Package{
-									{
-										Name:    "rails",
-										Version: "4.0.2",
-										Layer: ftypes.Layer{
-											DiffID: "sha256:0ea33a93585cf1917ba522b2304634c3073654062d5282c1346322967790ef33",
-										},
-									},
+									railsPkg,
 								},
 							},
 						},
@@ -94,11 +132,14 @@ func TestScanner_Scan(t *testing.T) {
 					Target: "alpine:latest (alpine 3.11)",
 					Class:  types.ClassOSPkg,
 					Type:   ftypes.Alpine,
+					Packages: ftypes.Packages{
+						muslPkg,
+					},
 					Vulnerabilities: []types.DetectedVulnerability{
 						{
 							VulnerabilityID:  "CVE-2020-9999",
-							PkgName:          "musl",
-							InstalledVersion: "1.2.3",
+							PkgName:          muslPkg.Name,
+							InstalledVersion: muslPkg.Version,
 							FixedVersion:     "1.2.4",
 							Status:           dbTypes.StatusFixed,
 							Layer: ftypes.Layer{
@@ -117,11 +158,14 @@ func TestScanner_Scan(t *testing.T) {
 					Target: "/app/Gemfile.lock",
 					Class:  types.ClassLangPkg,
 					Type:   ftypes.Bundler,
+					Packages: ftypes.Packages{
+						railsPkg,
+					},
 					Vulnerabilities: []types.DetectedVulnerability{
 						{
 							VulnerabilityID:  "CVE-2014-0081",
-							PkgName:          "rails",
-							InstalledVersion: "4.0.2",
+							PkgName:          railsPkg.Name,
+							InstalledVersion: railsPkg.Version,
 							FixedVersion:     "4.0.3, 3.2.17",
 							Status:           dbTypes.StatusFixed,
 							Layer: ftypes.Layer{
@@ -169,46 +213,21 @@ func TestScanner_Scan(t *testing.T) {
 							Name:   "3.11",
 						},
 						Packages: []ftypes.Package{
-							{
-								Name:       "musl",
-								Version:    "1.2.3",
-								SrcName:    "musl",
-								SrcVersion: "1.2.3",
-								Licenses:   []string{"MIT"},
-								Layer: ftypes.Layer{
-									DiffID: "sha256:ebf12965380b39889c99a9c02e82ba465f887b45975b6e389d42e9e6a3857888",
-								},
-							},
+							muslPkg,
 						},
 						Applications: []ftypes.Application{
 							{
 								Type:     ftypes.GoModule,
 								FilePath: "/app/go.mod",
 								Packages: []ftypes.Package{
-									{
-										Name:     "github.com/google/uuid",
-										Version:  "1.6.0",
-										FilePath: "",
-										Layer: ftypes.Layer{
-											DiffID: "sha256:0ea33a93585cf1917ba522b2304634c3073654062d5282c1346322967790ef33",
-										},
-										Licenses: []string{"LGPL"},
-									},
+									uuidPkg,
 								},
 							},
 							{
 								Type:     ftypes.PythonPkg,
 								FilePath: "",
 								Packages: []ftypes.Package{
-									{
-										Name:     "urllib3",
-										Version:  "3.2.1",
-										FilePath: "/usr/lib/python/site-packages/urllib3-3.2.1/METADATA",
-										Layer: ftypes.Layer{
-											DiffID: "sha256:0ea33a93585cf1917ba522b2304634c3073654062d5282c1346322967790ef33",
-										},
-										Licenses: []string{"MIT"},
-									},
+									urllib3Pkg,
 								},
 							},
 						},
@@ -223,7 +242,7 @@ func TestScanner_Scan(t *testing.T) {
 						{
 							Severity:   "UNKNOWN",
 							Category:   "unknown",
-							PkgName:    "musl",
+							PkgName:    muslPkg.Name,
 							Name:       "MIT",
 							Confidence: 1,
 						},
@@ -236,7 +255,7 @@ func TestScanner_Scan(t *testing.T) {
 						{
 							Severity:   "UNKNOWN",
 							Category:   "unknown",
-							PkgName:    "github.com/google/uuid",
+							PkgName:    uuidPkg.Name,
 							FilePath:   "/app/go.mod",
 							Name:       "LGPL",
 							Confidence: 1,
@@ -251,7 +270,7 @@ func TestScanner_Scan(t *testing.T) {
 						{
 							Severity:   "UNKNOWN",
 							Category:   "unknown",
-							PkgName:    "urllib3",
+							PkgName:    urllib3Pkg.Name,
 							FilePath:   "/usr/lib/python/site-packages/urllib3-3.2.1/METADATA",
 							Name:       "MIT",
 							Confidence: 1,
@@ -269,268 +288,6 @@ func TestScanner_Scan(t *testing.T) {
 				Eosl:   false,
 			},
 		},
-		{
-			name: "happy path with list all packages",
-			args: args{
-				target:   "alpine:latest",
-				layerIDs: []string{"sha256:5216338b40a7b96416b8b9858974bbe4acc3096ee60acbc4dfb1ee02aecceb10"},
-				options: types.ScanOptions{
-					VulnType: []string{
-						types.VulnTypeOS,
-						types.VulnTypeLibrary,
-					},
-					Scanners:        types.Scanners{types.VulnerabilityScanner},
-					ListAllPackages: true,
-				},
-			},
-			fixtures: []string{"testdata/fixtures/happy.yaml"},
-			applyLayersExpectation: ApplierApplyLayersExpectation{
-				Args: ApplierApplyLayersArgs{
-					BlobIDs: []string{"sha256:5216338b40a7b96416b8b9858974bbe4acc3096ee60acbc4dfb1ee02aecceb10"},
-				},
-				Returns: ApplierApplyLayersReturns{
-					Detail: ftypes.ArtifactDetail{
-						OS: ftypes.OS{
-							Family: "alpine",
-							Name:   "3.11",
-						},
-						Packages: []ftypes.Package{
-							{
-								Name:       "musl",
-								Version:    "1.2.3",
-								SrcName:    "musl",
-								SrcVersion: "1.2.3",
-								Layer: ftypes.Layer{
-									DiffID: "sha256:ebf12965380b39889c99a9c02e82ba465f887b45975b6e389d42e9e6a3857888",
-								},
-							},
-							{
-								Name:       "ausl",
-								Version:    "1.2.3",
-								SrcName:    "ausl",
-								SrcVersion: "1.2.3",
-								Layer: ftypes.Layer{
-									DiffID: "sha256:bbf12965380b39889c99a9c02e82ba465f887b45975b6e389d42e9e6a3857888",
-								},
-							},
-						},
-						Applications: []ftypes.Application{
-							{
-								Type:     "bundler",
-								FilePath: "/app/Gemfile.lock",
-								Packages: []ftypes.Package{
-									{
-										Name:    "rails",
-										Version: "4.0.2",
-										Layer: ftypes.Layer{
-											DiffID: "sha256:0ea33a93585cf1917ba522b2304634c3073654062d5282c1346322967790ef33",
-										},
-									},
-								},
-							},
-						},
-					},
-				},
-			},
-			wantResults: types.Results{
-				{
-					Target: "alpine:latest (alpine 3.11)",
-					Class:  types.ClassOSPkg,
-					Type:   ftypes.Alpine,
-					Packages: []ftypes.Package{
-						{
-							Name:       "ausl",
-							Version:    "1.2.3",
-							SrcName:    "ausl",
-							SrcVersion: "1.2.3",
-							Layer: ftypes.Layer{
-								DiffID: "sha256:bbf12965380b39889c99a9c02e82ba465f887b45975b6e389d42e9e6a3857888",
-							},
-						},
-						{
-							Name:       "musl",
-							Version:    "1.2.3",
-							SrcName:    "musl",
-							SrcVersion: "1.2.3",
-							Layer: ftypes.Layer{
-								DiffID: "sha256:ebf12965380b39889c99a9c02e82ba465f887b45975b6e389d42e9e6a3857888",
-							},
-						},
-					},
-					// For backward compatibility, will be removed
-					Vulnerabilities: []types.DetectedVulnerability{
-						{
-							VulnerabilityID:  "CVE-2020-9999",
-							PkgName:          "musl",
-							InstalledVersion: "1.2.3",
-							FixedVersion:     "1.2.4",
-							Status:           dbTypes.StatusFixed,
-							Layer: ftypes.Layer{
-								DiffID: "sha256:ebf12965380b39889c99a9c02e82ba465f887b45975b6e389d42e9e6a3857888",
-							},
-							PrimaryURL: "https://avd.aquasec.com/nvd/cve-2020-9999",
-							Vulnerability: dbTypes.Vulnerability{
-								Title:       "dos",
-								Description: "dos vulnerability",
-								Severity:    "HIGH",
-							},
-						},
-					},
-				},
-				{
-					Target: "/app/Gemfile.lock",
-					Class:  types.ClassLangPkg,
-					Type:   ftypes.Bundler,
-					Packages: []ftypes.Package{
-						{
-							Name:    "rails",
-							Version: "4.0.2",
-							Layer: ftypes.Layer{
-								DiffID: "sha256:0ea33a93585cf1917ba522b2304634c3073654062d5282c1346322967790ef33",
-							},
-						},
-					},
-					// For backward compatibility, will be removed
-					Vulnerabilities: []types.DetectedVulnerability{
-						{
-							VulnerabilityID:  "CVE-2014-0081",
-							PkgName:          "rails",
-							InstalledVersion: "4.0.2",
-							FixedVersion:     "4.0.3, 3.2.17",
-							Status:           dbTypes.StatusFixed,
-							Layer: ftypes.Layer{
-								DiffID: "sha256:0ea33a93585cf1917ba522b2304634c3073654062d5282c1346322967790ef33",
-							},
-							PrimaryURL: "https://avd.aquasec.com/nvd/cve-2014-0081",
-							Vulnerability: dbTypes.Vulnerability{
-								Title:       "xss",
-								Description: "xss vulnerability",
-								Severity:    "MEDIUM",
-								References: []string{
-									"http://example.com",
-								},
-								LastModifiedDate: lo.ToPtr(time.Date(2020, 2, 1, 1, 1, 0, 0, time.UTC)),
-								PublishedDate:    lo.ToPtr(time.Date(2020, 1, 1, 1, 1, 0, 0, time.UTC)),
-							},
-						},
-					},
-				},
-			},
-			wantOS: ftypes.OS{
-				Family: "alpine",
-				Name:   "3.11",
-				Eosl:   true,
-			},
-		},
-		{
-			name: "happy path with list all packages and without vulnerabilities",
-			args: args{
-				target:   "alpine:latest",
-				layerIDs: []string{"sha256:5216338b40a7b96416b8b9858974bbe4acc3096ee60acbc4dfb1ee02aecceb10"},
-				options: types.ScanOptions{
-					VulnType: []string{
-						types.VulnTypeOS,
-						types.VulnTypeLibrary,
-					},
-					Scanners:        types.Scanners{types.VulnerabilityScanner},
-					ListAllPackages: true,
-				},
-			},
-			applyLayersExpectation: ApplierApplyLayersExpectation{
-				Args: ApplierApplyLayersArgs{
-					BlobIDs: []string{"sha256:5216338b40a7b96416b8b9858974bbe4acc3096ee60acbc4dfb1ee02aecceb10"},
-				},
-				Returns: ApplierApplyLayersReturns{
-					Detail: ftypes.ArtifactDetail{
-						OS: ftypes.OS{
-							Family: "alpine",
-							Name:   "3.11",
-						},
-						Packages: []ftypes.Package{
-							{
-								Name:       "musl",
-								Version:    "1.2.3",
-								SrcName:    "musl",
-								SrcVersion: "1.2.3",
-								Layer: ftypes.Layer{
-									DiffID: "sha256:ebf12965380b39889c99a9c02e82ba465f887b45975b6e389d42e9e6a3857888",
-								},
-							},
-							{
-								Name:       "ausl",
-								Version:    "1.2.3",
-								SrcName:    "ausl",
-								SrcVersion: "1.2.3",
-								Layer: ftypes.Layer{
-									DiffID: "sha256:bbf12965380b39889c99a9c02e82ba465f887b45975b6e389d42e9e6a3857888",
-								},
-							},
-						},
-						Applications: []ftypes.Application{
-							{
-								Type:     "bundler",
-								FilePath: "/app/Gemfile.lock",
-								Packages: []ftypes.Package{
-									{
-										Name:    "rails",
-										Version: "4.0.2",
-										Layer: ftypes.Layer{
-											DiffID: "sha256:0ea33a93585cf1917ba522b2304634c3073654062d5282c1346322967790ef33",
-										},
-									},
-								},
-							},
-						},
-					},
-				},
-			},
-			wantResults: types.Results{
-				{
-					Target: "alpine:latest (alpine 3.11)",
-					Class:  types.ClassOSPkg,
-					Type:   ftypes.Alpine,
-					Packages: []ftypes.Package{
-						{
-							Name:       "ausl",
-							Version:    "1.2.3",
-							SrcName:    "ausl",
-							SrcVersion: "1.2.3",
-							Layer: ftypes.Layer{
-								DiffID: "sha256:bbf12965380b39889c99a9c02e82ba465f887b45975b6e389d42e9e6a3857888",
-							},
-						},
-						{
-							Name:       "musl",
-							Version:    "1.2.3",
-							SrcName:    "musl",
-							SrcVersion: "1.2.3",
-							Layer: ftypes.Layer{
-								DiffID: "sha256:ebf12965380b39889c99a9c02e82ba465f887b45975b6e389d42e9e6a3857888",
-							},
-						},
-					},
-				},
-				{
-					Target: "/app/Gemfile.lock",
-					Class:  types.ClassLangPkg,
-					Type:   ftypes.Bundler,
-					Packages: []ftypes.Package{
-						{
-							Name:    "rails",
-							Version: "4.0.2",
-							Layer: ftypes.Layer{
-								DiffID: "sha256:0ea33a93585cf1917ba522b2304634c3073654062d5282c1346322967790ef33",
-							},
-						},
-					},
-				},
-			},
-			wantOS: ftypes.OS{
-				Family: "alpine",
-				Name:   "3.11",
-				Eosl:   true,
-			},
-		},
 		{
 			name: "happy path with empty os",
 			args: args{
@@ -555,28 +312,16 @@ func TestScanner_Scan(t *testing.T) {
 						Applications: []ftypes.Application{
 							{
 								Type:     ftypes.Bundler,
-								FilePath: "/app/Gemfile.lock",
+								FilePath: "/app1/Gemfile.lock",
 								Packages: []ftypes.Package{
-									{
-										Name:    "innocent", // no vulnerability
-										Version: "1.2.3",
-										Layer: ftypes.Layer{
-											DiffID: "sha256:9922bc15eeefe1637b803ef2106f178152ce19a391f24aec838cbe2e48e73303",
-										},
-									},
+									innocentPkg, // no vulnerability
 								},
 							},
 							{
 								Type:     ftypes.Bundler,
-								FilePath: "/app/Gemfile.lock",
+								FilePath: "/app2/Gemfile.lock",
 								Packages: []ftypes.Package{
-									{
-										Name:    "rails", // one vulnerability
-										Version: "4.0.2",
-										Layer: ftypes.Layer{
-											DiffID: "sha256:9922bc15eeefe1637b803ef2106f178152ce19a391f24aec838cbe2e48e73303",
-										},
-									},
+									railsPkg, // one vulnerability
 								},
 							},
 						},
@@ -585,18 +330,29 @@ func TestScanner_Scan(t *testing.T) {
 			},
 			wantResults: types.Results{
 				{
-					Target: "/app/Gemfile.lock",
+					Target: "/app1/Gemfile.lock",
 					Class:  types.ClassLangPkg,
-					Type:   "bundler",
+					Type:   ftypes.Bundler,
+					Packages: ftypes.Packages{
+						innocentPkg,
+					},
+				},
+				{
+					Target: "/app2/Gemfile.lock",
+					Class:  types.ClassLangPkg,
+					Type:   ftypes.Bundler,
+					Packages: ftypes.Packages{
+						railsPkg,
+					},
 					Vulnerabilities: []types.DetectedVulnerability{
 						{
 							VulnerabilityID:  "CVE-2014-0081",
-							PkgName:          "rails",
-							InstalledVersion: "4.0.2",
+							PkgName:          railsPkg.Name,
+							InstalledVersion: railsPkg.Version,
 							FixedVersion:     "4.0.3, 3.2.17",
 							Status:           dbTypes.StatusFixed,
 							Layer: ftypes.Layer{
-								DiffID: "sha256:9922bc15eeefe1637b803ef2106f178152ce19a391f24aec838cbe2e48e73303",
+								DiffID: "sha256:0ea33a93585cf1917ba522b2304634c3073654062d5282c1346322967790ef33",
 							},
 							PrimaryURL: "https://avd.aquasec.com/nvd/cve-2014-0081",
 							Vulnerability: dbTypes.Vulnerability{
@@ -621,9 +377,8 @@ func TestScanner_Scan(t *testing.T) {
 				target:   "./result.cdx",
 				layerIDs: []string{"sha256:5216338b40a7b96416b8b9858974bbe4acc3096ee60acbc4dfb1ee02aecceb10"},
 				options: types.ScanOptions{
-					VulnType:        []string{types.VulnTypeLibrary},
-					Scanners:        types.Scanners{types.VulnerabilityScanner},
-					ListAllPackages: true,
+					VulnType: []string{types.VulnTypeLibrary},
+					Scanners: types.Scanners{types.VulnerabilityScanner},
 				},
 			},
 			fixtures: []string{"testdata/fixtures/happy.yaml"},
@@ -741,13 +496,7 @@ func TestScanner_Scan(t *testing.T) {
 								Type:     "bundler",
 								FilePath: "/app/Gemfile.lock",
 								Packages: []ftypes.Package{
-									{
-										Name:    "rails",
-										Version: "4.0.2",
-										Layer: ftypes.Layer{
-											DiffID: "sha256:0ea33a93585cf1917ba522b2304634c3073654062d5282c1346322967790ef33",
-										},
-									},
+									railsPkg,
 								},
 							},
 						},
@@ -765,6 +514,9 @@ func TestScanner_Scan(t *testing.T) {
 					Target: "/app/Gemfile.lock",
 					Class:  types.ClassLangPkg,
 					Type:   ftypes.Bundler,
+					Packages: ftypes.Packages{
+						railsPkg,
+					},
 					Vulnerabilities: []types.DetectedVulnerability{
 						{
 							VulnerabilityID:  "CVE-2014-0081",
@@ -822,16 +574,10 @@ func TestScanner_Scan(t *testing.T) {
 						},
 						Applications: []ftypes.Application{
 							{
-								Type:     "bundler",
+								Type:     ftypes.Bundler,
 								FilePath: "/app/Gemfile.lock",
 								Packages: []ftypes.Package{
-									{
-										Name:    "rails",
-										Version: "4.0.2",
-										Layer: ftypes.Layer{
-											DiffID: "sha256:9922bc15eeefe1637b803ef2106f178152ce19a391f24aec838cbe2e48e73303",
-										},
-									},
+									railsPkg,
 								},
 							},
 						},
@@ -840,18 +586,19 @@ func TestScanner_Scan(t *testing.T) {
 			},
 			wantResults: types.Results{
 				{
-					Target: "/app/Gemfile.lock",
-					Class:  types.ClassLangPkg,
-					Type:   ftypes.Bundler,
+					Target:   "/app/Gemfile.lock",
+					Class:    types.ClassLangPkg,
+					Type:     ftypes.Bundler,
+					Packages: ftypes.Packages{railsPkg},
 					Vulnerabilities: []types.DetectedVulnerability{
 						{
 							VulnerabilityID:  "CVE-2014-0081",
-							PkgName:          "rails",
-							InstalledVersion: "4.0.2",
+							PkgName:          railsPkg.Name,
+							InstalledVersion: railsPkg.Version,
 							FixedVersion:     "4.0.3, 3.2.17",
 							Status:           dbTypes.StatusFixed,
 							Layer: ftypes.Layer{
-								DiffID: "sha256:9922bc15eeefe1637b803ef2106f178152ce19a391f24aec838cbe2e48e73303",
+								DiffID: "sha256:0ea33a93585cf1917ba522b2304634c3073654062d5282c1346322967790ef33",
 							},
 							PrimaryURL: "https://avd.aquasec.com/nvd/cve-2014-0081",
 							Vulnerability: dbTypes.Vulnerability{
@@ -901,7 +648,7 @@ func TestScanner_Scan(t *testing.T) {
 			name: "happy path with only language-specific package detection",
 			args: args{
 				target:   "alpine:latest",
-				layerIDs: []string{"sha256:5216338b40a7b96416b8b9858974bbe4acc3096ee60acbc4dfb1ee02aecceb10"},
+				layerIDs: []string{"sha256:0ea33a93585cf1917ba522b2304634c3073654062d5282c1346322967790ef33"},
 				options: types.ScanOptions{
 					VulnType: []string{types.VulnTypeLibrary},
 					Scanners: types.Scanners{types.VulnerabilityScanner},
@@ -910,7 +657,7 @@ func TestScanner_Scan(t *testing.T) {
 			fixtures: []string{"testdata/fixtures/happy.yaml"},
 			applyLayersExpectation: ApplierApplyLayersExpectation{
 				Args: ApplierApplyLayersArgs{
-					BlobIDs: []string{"sha256:5216338b40a7b96416b8b9858974bbe4acc3096ee60acbc4dfb1ee02aecceb10"},
+					BlobIDs: []string{"sha256:0ea33a93585cf1917ba522b2304634c3073654062d5282c1346322967790ef33"},
 				},
 				Returns: ApplierApplyLayersReturns{
 					Detail: ftypes.ArtifactDetail{
@@ -919,38 +666,21 @@ func TestScanner_Scan(t *testing.T) {
 							Name:   "3.11",
 						},
 						Packages: []ftypes.Package{
-							{
-								Name:       "musl",
-								Version:    "1.2.3",
-								SrcName:    "musl",
-								SrcVersion: "1.2.3",
-							},
+							muslPkg,
 						},
 						Applications: []ftypes.Application{
 							{
 								Type:     "bundler",
 								FilePath: "/app/Gemfile.lock",
 								Packages: []ftypes.Package{
-									{
-										Name:    "rails",
-										Version: "4.0.2",
-										Layer: ftypes.Layer{
-											DiffID: "sha256:5cb2a5009179b1e78ecfef81a19756328bb266456cf9a9dbbcf9af8b83b735f0",
-										},
-									},
+									railsPkg,
 								},
 							},
 							{
 								Type:     "composer",
 								FilePath: "/app/composer-lock.json",
 								Packages: []ftypes.Package{
-									{
-										Name:    "laravel/framework",
-										Version: "6.0.0",
-										Layer: ftypes.Layer{
-											DiffID: "sha256:9922bc15eeefe1637b803ef2106f178152ce19a391f24aec838cbe2e48e73303",
-										},
-									},
+									laravelPkg,
 								},
 							},
 						},
@@ -959,18 +689,19 @@ func TestScanner_Scan(t *testing.T) {
 			},
 			wantResults: types.Results{
 				{
-					Target: "/app/Gemfile.lock",
-					Class:  types.ClassLangPkg,
-					Type:   ftypes.Bundler,
+					Target:   "/app/Gemfile.lock",
+					Class:    types.ClassLangPkg,
+					Type:     ftypes.Bundler,
+					Packages: ftypes.Packages{railsPkg},
 					Vulnerabilities: []types.DetectedVulnerability{
 						{
 							VulnerabilityID:  "CVE-2014-0081",
-							PkgName:          "rails",
-							InstalledVersion: "4.0.2",
+							PkgName:          railsPkg.Name,
+							InstalledVersion: railsPkg.Version,
 							FixedVersion:     "4.0.3, 3.2.17",
 							Status:           dbTypes.StatusFixed,
 							Layer: ftypes.Layer{
-								DiffID: "sha256:5cb2a5009179b1e78ecfef81a19756328bb266456cf9a9dbbcf9af8b83b735f0",
+								DiffID: "sha256:0ea33a93585cf1917ba522b2304634c3073654062d5282c1346322967790ef33",
 							},
 							PrimaryURL: "https://avd.aquasec.com/nvd/cve-2014-0081",
 							Vulnerability: dbTypes.Vulnerability{
@@ -987,18 +718,19 @@ func TestScanner_Scan(t *testing.T) {
 					},
 				},
 				{
-					Target: "/app/composer-lock.json",
-					Class:  types.ClassLangPkg,
-					Type:   ftypes.Composer,
+					Target:   "/app/composer-lock.json",
+					Class:    types.ClassLangPkg,
+					Type:     ftypes.Composer,
+					Packages: ftypes.Packages{laravelPkg},
 					Vulnerabilities: []types.DetectedVulnerability{
 						{
 							VulnerabilityID:  "CVE-2021-21263",
-							PkgName:          "laravel/framework",
-							InstalledVersion: "6.0.0",
+							PkgName:          laravelPkg.Name,
+							InstalledVersion: laravelPkg.Version,
 							FixedVersion:     "8.22.1, 7.30.3, 6.20.12",
 							Status:           dbTypes.StatusFixed,
 							Layer: ftypes.Layer{
-								DiffID: "sha256:9922bc15eeefe1637b803ef2106f178152ce19a391f24aec838cbe2e48e73303",
+								DiffID: "sha256:0ea33a93585cf1917ba522b2304634c3073654062d5282c1346322967790ef33",
 							},
 						},
 					},
diff --git a/pkg/scanner/ospkg/scan.go b/pkg/scanner/ospkg/scan.go
index fee369e369e4..fb6c5719b887 100644
--- a/pkg/scanner/ospkg/scan.go
+++ b/pkg/scanner/ospkg/scan.go
@@ -42,10 +42,8 @@ func (s *scanner) Scan(ctx context.Context, target types.ScanTarget, opts types.
 		Type:   target.OS.Family,
 	}
 
-	if opts.ListAllPackages {
-		sort.Sort(target.Packages)
-		result.Packages = target.Packages
-	}
+	sort.Sort(target.Packages)
+	result.Packages = target.Packages
 
 	if !opts.Scanners.Enabled(types.VulnerabilityScanner) {
 		// Return packages only
diff --git a/pkg/types/scan.go b/pkg/types/scan.go
index 0b5833b12faa..04b6d6230230 100644
--- a/pkg/types/scan.go
+++ b/pkg/types/scan.go
@@ -26,7 +26,6 @@ type ScanOptions struct {
 	Scanners            Scanners
 	ImageConfigScanners Scanners // Scanners for container image configuration
 	ScanRemovedPackages bool
-	ListAllPackages     bool
 	LicenseCategories   map[types.LicenseCategory][]string
 	FilePatterns        []string
 	IncludeDevDeps      bool
diff --git a/pkg/types/target.go b/pkg/types/target.go
index 134bded69cd7..26386b9d2429 100644
--- a/pkg/types/target.go
+++ b/pkg/types/target.go
@@ -29,6 +29,9 @@ const (
 	// NoneScanner is the scanner of none
 	NoneScanner = Scanner("none")
 
+	// SBOMScanner is the virtual scanner of SBOM, which cannot be enabled by the user
+	SBOMScanner = Scanner("sbom")
+
 	// VulnerabilityScanner is the scanner of vulnerabilities
 	VulnerabilityScanner = Scanner("vuln")
 
@@ -70,12 +73,18 @@ var (
 	}
 )
 
-func (scanners Scanners) Enabled(s Scanner) bool {
-	return slices.Contains(scanners, s)
+func (scanners *Scanners) Enable(s Scanner) {
+	if !scanners.Enabled(s) {
+		*scanners = append(*scanners, s)
+	}
+}
+
+func (scanners *Scanners) Enabled(s Scanner) bool {
+	return slices.Contains(*scanners, s)
 }
 
 // AnyEnabled returns true if any of the passed scanners is included.
-func (scanners Scanners) AnyEnabled(ss ...Scanner) bool {
+func (scanners *Scanners) AnyEnabled(ss ...Scanner) bool {
 	for _, s := range ss {
 		if scanners.Enabled(s) {
 			return true
diff --git a/rpc/scanner/service.pb.go b/rpc/scanner/service.pb.go
index eb75c1d582b6..50d0ead38681 100644
--- a/rpc/scanner/service.pb.go
+++ b/rpc/scanner/service.pb.go
@@ -1,6 +1,6 @@
 // Code generated by protoc-gen-go. DO NOT EDIT.
 // versions:
-// 	protoc-gen-go v1.27.1
+// 	protoc-gen-go v1.34.0
 // 	protoc        v3.19.4
 // source: rpc/scanner/service.proto
 
@@ -148,7 +148,6 @@ type ScanOptions struct {
 
 	VulnType          []string             `protobuf:"bytes,1,rep,name=vuln_type,json=vulnType,proto3" json:"vuln_type,omitempty"`
 	Scanners          []string             `protobuf:"bytes,2,rep,name=scanners,proto3" json:"scanners,omitempty"`
-	ListAllPackages   bool                 `protobuf:"varint,3,opt,name=list_all_packages,json=listAllPackages,proto3" json:"list_all_packages,omitempty"`
 	LicenseCategories map[string]*Licenses `protobuf:"bytes,4,rep,name=license_categories,json=licenseCategories,proto3" json:"license_categories,omitempty" protobuf_key:"bytes,1,opt,name=key,proto3" protobuf_val:"bytes,2,opt,name=value,proto3"`
 	IncludeDevDeps    bool                 `protobuf:"varint,5,opt,name=include_dev_deps,json=includeDevDeps,proto3" json:"include_dev_deps,omitempty"`
 }
@@ -199,13 +198,6 @@ func (x *ScanOptions) GetScanners() []string {
 	return nil
 }
 
-func (x *ScanOptions) GetListAllPackages() bool {
-	if x != nil {
-		return x.ListAllPackages
-	}
-	return false
-}
-
 func (x *ScanOptions) GetLicenseCategories() map[string]*Licenses {
 	if x != nil {
 		return x.LicenseCategories
@@ -406,74 +398,72 @@ var file_rpc_scanner_service_proto_rawDesc = []byte{
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 }
 
 var (
diff --git a/rpc/scanner/service.proto b/rpc/scanner/service.proto
index 63f98d2779c6..312930adc89a 100644
--- a/rpc/scanner/service.proto
+++ b/rpc/scanner/service.proto
@@ -25,9 +25,10 @@ message Licenses {
 message ScanOptions {
   repeated string       vuln_type          = 1;
   repeated string       scanners           = 2;
-  bool                  list_all_packages  = 3;
   map<string, Licenses> license_categories = 4;
   bool                  include_dev_deps   = 5;
+
+  reserved 3;  // deleted 'list_all_packages'
 }
 
 message ScanResponse {
diff --git a/rpc/scanner/service.twirp.go b/rpc/scanner/service.twirp.go
index 4c88aec5db46..0a2fbe5759e7 100644
--- a/rpc/scanner/service.twirp.go
+++ b/rpc/scanner/service.twirp.go
@@ -1094,47 +1094,46 @@ func callClientError(ctx context.Context, h *twirp.ClientHooks, err twirp.Error)
 }
 
 var twirpFileDescriptor0 = []byte{
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 }