diff --git a/NEXT_CHANGELOG.md b/NEXT_CHANGELOG.md
index 2c07236abf0..76267ac144d 100644
--- a/NEXT_CHANGELOG.md
+++ b/NEXT_CHANGELOG.md
@@ -12,6 +12,7 @@
 
  * `bundle generate job` now downloads workspace files referenced by `spark_python_task`, rewriting them to a relative path like it already does for notebooks. Git-sourced files and cloud URIs are left untouched ([#5799](https://github.com/databricks/cli/pull/5799)).
 * Fix permissions added to a job or pipeline by a Python (PyDABs) mutator failing to deploy with "must have exactly one owner"; the deploying identity is now set as owner, matching resources whose permissions are declared in YAML ([#5821](https://github.com/databricks/cli/pull/5821)).
+* `bundle generate` now warns when the generated configuration file is not matched by any pattern in the `include` section of `databricks.yml` ([#XXXX](https://github.com/databricks/cli/pull/XXXX)).
 
 ### Dependency updates
 
diff --git a/acceptance/bundle/generate/alert/output.txt b/acceptance/bundle/generate/alert/output.txt
index d6482446e33..8503daa3568 100644
--- a/acceptance/bundle/generate/alert/output.txt
+++ b/acceptance/bundle/generate/alert/output.txt
@@ -4,3 +4,11 @@
 >>> [CLI] bundle generate alert --existing-id [ALERT_ID] --source-dir out/alert --config-dir out/resource
 Alert configuration successfully saved to [TEST_TMP_DIR]/out/resource/test_alert.alert.yml
 Serialized alert definition to [TEST_TMP_DIR]/out/alert/test_alert.dbalert.json
+Warning: Generated configuration is not included in the bundle
+
+The file out/resource/test_alert.alert.yml is not matched by any pattern in the 'include' section of databricks.yml,
+so it will not be deployed. Add a matching entry to the 'include' section, for example:
+
+include:
+  - out/resource/*.yml
+
diff --git a/acceptance/bundle/generate/app_not_yet_deployed/output.txt b/acceptance/bundle/generate/app_not_yet_deployed/output.txt
index bbfb51b291c..5742aab1b58 100644
--- a/acceptance/bundle/generate/app_not_yet_deployed/output.txt
+++ b/acceptance/bundle/generate/app_not_yet_deployed/output.txt
@@ -21,3 +21,11 @@
 >>> [CLI] bundle generate app --existing-app-name my-app --config-dir . --key out
 Loading app 'my-app' configuration
 App configuration successfully saved to out.app.yml
+Warning: Generated configuration is not included in the bundle
+
+The file out.app.yml is not matched by any pattern in the 'include' section of databricks.yml,
+so it will not be deployed. Add a matching entry to the 'include' section, for example:
+
+include:
+  - *.yml
+
diff --git a/acceptance/bundle/generate/app_subfolders/output.txt b/acceptance/bundle/generate/app_subfolders/output.txt
index 654d38ed1d6..40c2705cae3 100644
--- a/acceptance/bundle/generate/app_subfolders/output.txt
+++ b/acceptance/bundle/generate/app_subfolders/output.txt
@@ -1,3 +1,11 @@
 Loading app 'my_app' configuration
 File successfully saved to out/sub/folder/1.py
 App configuration successfully saved to out.app.yml
+Warning: Generated configuration is not included in the bundle
+
+The file out.app.yml is not matched by any pattern in the 'include' section of databricks.yml,
+so it will not be deployed. Add a matching entry to the 'include' section, for example:
+
+include:
+  - *.yml
+
diff --git a/acceptance/bundle/generate/dashboard/output.txt b/acceptance/bundle/generate/dashboard/output.txt
index 07a77e1097e..4ff194d800f 100644
--- a/acceptance/bundle/generate/dashboard/output.txt
+++ b/acceptance/bundle/generate/dashboard/output.txt
@@ -4,3 +4,11 @@
 >>> [CLI] bundle generate dashboard --existing-id [DASHBOARD_ID] --dashboard-dir out/dashboard --resource-dir out/resource
 Writing dashboard to out/dashboard/test_dashboard.lvdash.json
 Writing configuration to out/resource/test_dashboard.dashboard.yml
+Warning: Generated configuration is not included in the bundle
+
+The file out/resource/test_dashboard.dashboard.yml is not matched by any pattern in the 'include' section of databricks.yml,
+so it will not be deployed. Add a matching entry to the 'include' section, for example:
+
+include:
+  - out/resource/*.yml
+
diff --git a/acceptance/bundle/generate/dashboard_existing_path_nominal/output.txt b/acceptance/bundle/generate/dashboard_existing_path_nominal/output.txt
index dcef0efdf55..3b76a51c84b 100644
--- a/acceptance/bundle/generate/dashboard_existing_path_nominal/output.txt
+++ b/acceptance/bundle/generate/dashboard_existing_path_nominal/output.txt
@@ -2,7 +2,23 @@
 >>> [CLI] bundle generate dashboard --existing-path /path/to/dashboard --dashboard-dir out/dashboard --resource-dir out/resource
 Writing dashboard to out/dashboard/this_is_a_test_dashboard.lvdash.json
 Writing configuration to out/resource/this_is_a_test_dashboard.dashboard.yml
+Warning: Generated configuration is not included in the bundle
+
+The file out/resource/this_is_a_test_dashboard.dashboard.yml is not matched by any pattern in the 'include' section of databricks.yml,
+so it will not be deployed. Add a matching entry to the 'include' section, for example:
+
+include:
+  - out/resource/*.yml
+
 
 >>> [CLI] bundle generate dashboard --existing-path /path/to/dashboard --key custom_key --dashboard-dir out/dashboard --resource-dir out/resource
 Writing dashboard to out/dashboard/custom_key.lvdash.json
 Writing configuration to out/resource/custom_key.dashboard.yml
+Warning: Generated configuration is not included in the bundle
+
+The file out/resource/custom_key.dashboard.yml is not matched by any pattern in the 'include' section of databricks.yml,
+so it will not be deployed. Add a matching entry to the 'include' section, for example:
+
+include:
+  - out/resource/*.yml
+
diff --git a/acceptance/bundle/generate/designer_job/output.txt b/acceptance/bundle/generate/designer_job/output.txt
index d0009533565..44c322537b7 100644
--- a/acceptance/bundle/generate/designer_job/output.txt
+++ b/acceptance/bundle/generate/designer_job/output.txt
@@ -1,2 +1,10 @@
 File successfully saved to outnotebook.designer.ipynb
 Job configuration successfully saved to out.job.yml
+Warning: Generated configuration is not included in the bundle
+
+The file out.job.yml is not matched by any pattern in the 'include' section of databricks.yml,
+so it will not be deployed. Add a matching entry to the 'include' section, for example:
+
+include:
+  - *.yml
+
diff --git a/acceptance/bundle/generate/genie_space/output.txt b/acceptance/bundle/generate/genie_space/output.txt
index a313a51adc3..68334c9c1d1 100644
--- a/acceptance/bundle/generate/genie_space/output.txt
+++ b/acceptance/bundle/generate/genie_space/output.txt
@@ -4,3 +4,11 @@
 >>> [CLI] bundle generate genie-space --existing-id [GENIE_SPACE_ID] --genie-space-dir out/genie_space --resource-dir out/resource
 Writing genie space to out/genie_space/test_genie_space.geniespace.json
 Writing configuration to out/resource/test_genie_space.genie_space.yml
+Warning: Generated configuration is not included in the bundle
+
+The file out/resource/test_genie_space.genie_space.yml is not matched by any pattern in the 'include' section of databricks.yml,
+so it will not be deployed. Add a matching entry to the 'include' section, for example:
+
+include:
+  - out/resource/*.yml
+
diff --git a/acceptance/bundle/generate/git_job/output.txt b/acceptance/bundle/generate/git_job/output.txt
index 680c92ff94a..864f53e7dc1 100644
--- a/acceptance/bundle/generate/git_job/output.txt
+++ b/acceptance/bundle/generate/git_job/output.txt
@@ -1,2 +1,10 @@
 Job is using Git source, skipping downloading files
 Job configuration successfully saved to out.job.yml
+Warning: Generated configuration is not included in the bundle
+
+The file out.job.yml is not matched by any pattern in the 'include' section of databricks.yml,
+so it will not be deployed. Add a matching entry to the 'include' section, for example:
+
+include:
+  - *.yml
+
diff --git a/acceptance/bundle/generate/include_warning/databricks.yml b/acceptance/bundle/generate/include_warning/databricks.yml
new file mode 100644
index 00000000000..4057cf2dd10
--- /dev/null
+++ b/acceptance/bundle/generate/include_warning/databricks.yml
@@ -0,0 +1,5 @@
+bundle:
+  name: include_warning
+
+include:
+  - resources/*.yml
diff --git a/acceptance/bundle/generate/include_warning/out.test.toml b/acceptance/bundle/generate/include_warning/out.test.toml
new file mode 100644
index 00000000000..f784a183258
--- /dev/null
+++ b/acceptance/bundle/generate/include_warning/out.test.toml
@@ -0,0 +1,3 @@
+Local = true
+Cloud = false
+EnvMatrix.DATABRICKS_BUNDLE_ENGINE = ["terraform", "direct"]
diff --git a/acceptance/bundle/generate/include_warning/output.txt b/acceptance/bundle/generate/include_warning/output.txt
new file mode 100644
index 00000000000..e9869179df8
--- /dev/null
+++ b/acceptance/bundle/generate/include_warning/output.txt
@@ -0,0 +1,16 @@
+
+>>> [CLI] bundle generate job --existing-job-id 1234 --config-dir resources --key included
+Job is using Git source, skipping downloading files
+Job configuration successfully saved to resources/included.job.yml
+
+>>> [CLI] bundle generate job --existing-job-id 1234 --config-dir subdir --key excluded
+Job is using Git source, skipping downloading files
+Job configuration successfully saved to subdir/excluded.job.yml
+Warning: Generated configuration is not included in the bundle
+
+The file subdir/excluded.job.yml is not matched by any pattern in the 'include' section of databricks.yml,
+so it will not be deployed. Add a matching entry to the 'include' section, for example:
+
+include:
+  - subdir/*.yml
+
diff --git a/acceptance/bundle/generate/include_warning/script b/acceptance/bundle/generate/include_warning/script
new file mode 100644
index 00000000000..87f7afeb37a
--- /dev/null
+++ b/acceptance/bundle/generate/include_warning/script
@@ -0,0 +1,11 @@
+# A resource generated into a directory matched by the 'include' section
+# is deployed, so no warning is emitted.
+trace $CLI bundle generate job --existing-job-id 1234 --config-dir resources --key included
+
+# A resource generated into a directory that no 'include' pattern matches is
+# written to disk but silently ignored during deploy, so we warn about it.
+trace $CLI bundle generate job --existing-job-id 1234 --config-dir subdir --key excluded
+
+# The generated config files are not asserted on here; remove them so they are
+# not reported as unexpected leftover files.
+rm -r resources subdir
diff --git a/acceptance/bundle/generate/include_warning/test.toml b/acceptance/bundle/generate/include_warning/test.toml
new file mode 100644
index 00000000000..3a137df700c
--- /dev/null
+++ b/acceptance/bundle/generate/include_warning/test.toml
@@ -0,0 +1,24 @@
+[[Server]]
+Pattern = "GET /api/2.2/jobs/get"
+Response.Body = '''
+{
+    "job_id": 11223344,
+    "settings": {
+        "name": "gitjob",
+        "git_source": {
+            "git_url":      "https://git.databricks.com",
+            "git_provider": "github",
+            "git_branch":   "main",
+            "git_commit":   "abcdef"
+        },
+        "tasks": [
+            {
+                "task_key": "test_task",
+                "notebook_task": {
+                    "notebook_path": "some/test/notebook.py"
+                }
+            }
+        ]
+    }
+}
+'''
diff --git a/acceptance/bundle/generate/ipynb_job/output.txt b/acceptance/bundle/generate/ipynb_job/output.txt
index 61273cbf63e..e88d09508dc 100644
--- a/acceptance/bundle/generate/ipynb_job/output.txt
+++ b/acceptance/bundle/generate/ipynb_job/output.txt
@@ -1,2 +1,10 @@
 File successfully saved to outnotebook.ipynb
 Job configuration successfully saved to out.job.yml
+Warning: Generated configuration is not included in the bundle
+
+The file out.job.yml is not matched by any pattern in the 'include' section of databricks.yml,
+so it will not be deployed. Add a matching entry to the 'include' section, for example:
+
+include:
+  - *.yml
+
diff --git a/acceptance/bundle/generate/job_nested_notebooks/output.txt b/acceptance/bundle/generate/job_nested_notebooks/output.txt
index f0b8326de09..c0615715c5c 100644
--- a/acceptance/bundle/generate/job_nested_notebooks/output.txt
+++ b/acceptance/bundle/generate/job_nested_notebooks/output.txt
@@ -1,6 +1,14 @@
 File successfully saved to src/my_folder/my_notebook.py
 File successfully saved to src/other_folder/other_notebook.py
 Job configuration successfully saved to out.job.yml
+Warning: Generated configuration is not included in the bundle
+
+The file out.job.yml is not matched by any pattern in the 'include' section of databricks.yml,
+so it will not be deployed. Add a matching entry to the 'include' section, for example:
+
+include:
+  - *.yml
+
 === old flattened files should be gone ===
 src/my_notebook.py removed
 src/other_notebook.py removed
diff --git a/acceptance/bundle/generate/job_nested_notebooks/script b/acceptance/bundle/generate/job_nested_notebooks/script
index 04805db6389..a52154efbb0 100644
--- a/acceptance/bundle/generate/job_nested_notebooks/script
+++ b/acceptance/bundle/generate/job_nested_notebooks/script
@@ -2,7 +2,13 @@ mkdir -p src
 echo "old" > src/my_notebook.py
 echo "old" > src/other_notebook.py
 
-$CLI bundle generate job --existing-job-id 1234 --config-dir . --key out --force --source-dir src 2>&1 | sort
+# The concurrent downloader emits the "File successfully saved" lines in
+# nondeterministic order, so sort just those; the remaining lines (including the
+# multi-line include warning) are deterministic and kept in their natural order.
+$CLI bundle generate job --existing-job-id 1234 --config-dir . --key out --force --source-dir src > out.gen.txt 2>&1
+grep '^File successfully saved to' out.gen.txt | sort
+grep -v '^File successfully saved to' out.gen.txt
+rm out.gen.txt
 
 echo "=== old flattened files should be gone ==="
 test ! -f src/my_notebook.py && echo "src/my_notebook.py removed" || echo "src/my_notebook.py still exists"
diff --git a/acceptance/bundle/generate/lakeflow_pipelines/output.txt b/acceptance/bundle/generate/lakeflow_pipelines/output.txt
index b4c4e3d60aa..fbef31fbbe5 100644
--- a/acceptance/bundle/generate/lakeflow_pipelines/output.txt
+++ b/acceptance/bundle/generate/lakeflow_pipelines/output.txt
@@ -1,4 +1,12 @@
 Pipeline configuration successfully saved to out/config/out.pipeline.yml
+Warning: Generated configuration is not included in the bundle
+
+The file out/config/out.pipeline.yml is not matched by any pattern in the 'include' section of databricks.yml,
+so it will not be deployed. Add a matching entry to the 'include' section, for example:
+
+include:
+  - out/config/*.yml
+
 File successfully saved to out/pipeline/explorations/1.py
 File successfully saved to out/pipeline/transformations/1.py
 File successfully saved to out/pipeline/transformations/2.py
diff --git a/acceptance/bundle/generate/pipeline/output.txt b/acceptance/bundle/generate/pipeline/output.txt
index e6cf41871c1..bd1d6d9031c 100644
--- a/acceptance/bundle/generate/pipeline/output.txt
+++ b/acceptance/bundle/generate/pipeline/output.txt
@@ -1,2 +1,10 @@
 File successfully saved to outnotebook.py
 Pipeline configuration successfully saved to out.pipeline.yml
+Warning: Generated configuration is not included in the bundle
+
+The file out.pipeline.yml is not matched by any pattern in the 'include' section of databricks.yml,
+so it will not be deployed. Add a matching entry to the 'include' section, for example:
+
+include:
+  - *.yml
+
diff --git a/acceptance/bundle/generate/pipeline_and_deploy/output.txt b/acceptance/bundle/generate/pipeline_and_deploy/output.txt
index 41c92d9ac10..02f5f7ad198 100644
--- a/acceptance/bundle/generate/pipeline_and_deploy/output.txt
+++ b/acceptance/bundle/generate/pipeline_and_deploy/output.txt
@@ -9,6 +9,14 @@
 === Generate bundle config from the pipelineFile successfully saved to src/notebook.py
 File successfully saved to src/test.py
 Pipeline configuration successfully saved to resources/out.pipeline.yml
+Warning: Generated configuration is not included in the bundle
+
+The file resources/out.pipeline.yml is not matched by any pattern in the 'include' section of databricks.yml,
+so it will not be deployed. Add a matching entry to the 'include' section, for example:
+
+include:
+  - resources/*.yml
+
 
 === Verify generated yaml has expected fields
 === Deploy the generated bundle
diff --git a/acceptance/bundle/generate/pipeline_and_deploy/script b/acceptance/bundle/generate/pipeline_and_deploy/script
index 85d9e044d5f..ab6b01e6764 100644
--- a/acceptance/bundle/generate/pipeline_and_deploy/script
+++ b/acceptance/bundle/generate/pipeline_and_deploy/script
@@ -32,7 +32,13 @@ cleanup() {
 trap cleanup EXIT
 
 title "Generate bundle config from the pipeline"
-$CLI bundle generate pipeline --existing-pipeline-id "$PIPELINE_ID" --key out --config-dir resources --source-dir src --force 2>&1 | sort
+# The concurrent downloader emits the "File successfully saved" lines in
+# nondeterministic order, so sort just those; the remaining lines (including the
+# multi-line include warning) are deterministic and kept in their natural order.
+$CLI bundle generate pipeline --existing-pipeline-id "$PIPELINE_ID" --key out --config-dir resources --source-dir src --force > out.gen.txt 2>&1
+grep '^File successfully saved to' out.gen.txt | sort
+grep -v '^File successfully saved to' out.gen.txt
+rm out.gen.txt
 
 title "Verify generated yaml has expected fields"
 cat resources/out.pipeline.yml | env -u MSYS_NO_PATHCONV contains.py "libraries:" "- notebook:" "path: ../src/notebook.py" "- file:" "path: ../src/test.py" > /dev/null
diff --git a/acceptance/bundle/generate/pipeline_with_glob/output.txt b/acceptance/bundle/generate/pipeline_with_glob/output.txt
index fbb2259bd26..fa9a5817593 100644
--- a/acceptance/bundle/generate/pipeline_with_glob/output.txt
+++ b/acceptance/bundle/generate/pipeline_with_glob/output.txt
@@ -1 +1,9 @@
 Pipeline configuration successfully saved to out.pipeline.yml
+Warning: Generated configuration is not included in the bundle
+
+The file out.pipeline.yml is not matched by any pattern in the 'include' section of databricks.yml,
+so it will not be deployed. Add a matching entry to the 'include' section, for example:
+
+include:
+  - *.yml
+
diff --git a/acceptance/bundle/generate/pipeline_with_sql/output.txt b/acceptance/bundle/generate/pipeline_with_sql/output.txt
index 3818255b6f9..230c4791b95 100644
--- a/acceptance/bundle/generate/pipeline_with_sql/output.txt
+++ b/acceptance/bundle/generate/pipeline_with_sql/output.txt
@@ -1,2 +1,10 @@
 File successfully saved to outsql.sql
 Pipeline configuration successfully saved to out.pipeline.yml
+Warning: Generated configuration is not included in the bundle
+
+The file out.pipeline.yml is not matched by any pattern in the 'include' section of databricks.yml,
+so it will not be deployed. Add a matching entry to the 'include' section, for example:
+
+include:
+  - *.yml
+
diff --git a/acceptance/bundle/generate/python_job/output.txt b/acceptance/bundle/generate/python_job/output.txt
index ad44285e3a9..28adf652f1d 100644
--- a/acceptance/bundle/generate/python_job/output.txt
+++ b/acceptance/bundle/generate/python_job/output.txt
@@ -1,2 +1,10 @@
 File successfully saved to outnotebook.py
 Job configuration successfully saved to out.job.yml
+Warning: Generated configuration is not included in the bundle
+
+The file out.job.yml is not matched by any pattern in the 'include' section of databricks.yml,
+so it will not be deployed. Add a matching entry to the 'include' section, for example:
+
+include:
+  - *.yml
+
diff --git a/acceptance/bundle/generate/python_job_and_deploy/output.txt b/acceptance/bundle/generate/python_job_and_deploy/output.txt
index aaa39b42448..8297c41e964 100644
--- a/acceptance/bundle/generate/python_job_and_deploy/output.txt
+++ b/acceptance/bundle/generate/python_job_and_deploy/output.txt
@@ -8,6 +8,14 @@
 >>> [CLI] bundle generate job --existing-job-id [JOB_ID] --key out --config-dir resources --source-dir src --force
 File successfully saved to src/test_notebook.py
 Job configuration successfully saved to resources/out.job.yml
+Warning: Generated configuration is not included in the bundle
+
+The file resources/out.job.yml is not matched by any pattern in the 'include' section of databricks.yml,
+so it will not be deployed. Add a matching entry to the 'include' section, for example:
+
+include:
+  - resources/*.yml
+
 
 === Verify generated yaml has expected fields
 === Deploy the generated bundle
diff --git a/acceptance/bundle/generate/spark_python_task_job/output.txt b/acceptance/bundle/generate/spark_python_task_job/output.txt
index e160a45625f..7bff1e49496 100644
--- a/acceptance/bundle/generate/spark_python_task_job/output.txt
+++ b/acceptance/bundle/generate/spark_python_task_job/output.txt
@@ -1,2 +1,10 @@
 File successfully saved to outjob.py
 Job configuration successfully saved to out.job.yml
+Warning: Generated configuration is not included in the bundle
+
+The file out.job.yml is not matched by any pattern in the 'include' section of databricks.yml,
+so it will not be deployed. Add a matching entry to the 'include' section, for example:
+
+include:
+  - *.yml
+
diff --git a/cmd/bundle/generate/alert.go b/cmd/bundle/generate/alert.go
index e80e559f319..cb78b24de1e 100644
--- a/cmd/bundle/generate/alert.go
+++ b/cmd/bundle/generate/alert.go
@@ -168,6 +168,8 @@ After generation, you can deploy this alert to other targets using:
 		cmdio.LogString(ctx, "Alert configuration successfully saved to "+filepath.ToSlash(configPath))
 		cmdio.LogString(ctx, "Serialized alert definition to "+filepath.ToSlash(alertPath))
 
+		warnIfNotIncluded(ctx, b, configPath)
+
 		return nil
 	}
 
diff --git a/cmd/bundle/generate/app.go b/cmd/bundle/generate/app.go
index 120c405e793..845853adbdf 100644
--- a/cmd/bundle/generate/app.go
+++ b/cmd/bundle/generate/app.go
@@ -128,6 +128,8 @@ per target environment.`,
 
 		cmdio.LogString(ctx, "App configuration successfully saved to "+filename)
 
+		warnIfNotIncluded(ctx, b, filename)
+
 		if bind {
 			return deployment.BindResource(cmd, appKey, app.Name, true, false, true)
 		}
diff --git a/cmd/bundle/generate/dashboard.go b/cmd/bundle/generate/dashboard.go
index 920d1064f01..086ec1d600a 100644
--- a/cmd/bundle/generate/dashboard.go
+++ b/cmd/bundle/generate/dashboard.go
@@ -251,6 +251,8 @@ func (d *dashboard) saveConfiguration(ctx context.Context, b *bundle.Bundle, das
 		return err
 	}
 
+	warnIfNotIncluded(ctx, b, resourcePath)
+
 	return nil
 }
 
diff --git a/cmd/bundle/generate/genie_space.go b/cmd/bundle/generate/genie_space.go
index 649f0cacc2c..6d938c5e03d 100644
--- a/cmd/bundle/generate/genie_space.go
+++ b/cmd/bundle/generate/genie_space.go
@@ -166,6 +166,8 @@ func (g *genieSpace) saveConfiguration(ctx context.Context, b *bundle.Bundle, ge
 		return err
 	}
 
+	warnIfNotIncluded(ctx, b, resourcePath)
+
 	return nil
 }
 
diff --git a/cmd/bundle/generate/include.go b/cmd/bundle/generate/include.go
new file mode 100644
index 00000000000..9801601ce23
--- /dev/null
+++ b/cmd/bundle/generate/include.go
@@ -0,0 +1,95 @@
+package generate
+
+import (
+	"context"
+	"fmt"
+	"path/filepath"
+
+	"github.com/databricks/cli/bundle"
+	"github.com/databricks/cli/bundle/config"
+	"github.com/databricks/cli/libs/diag"
+	"github.com/databricks/cli/libs/log"
+	"github.com/databricks/cli/libs/logdiag"
+)
+
+// warnIfNotIncluded warns when the freshly generated configuration file is not
+// matched by any pattern in the root databricks.yml 'include' section. Such a
+// file is written to disk but silently ignored during deploy, so without a
+// matching 'include' entry the generate command is effectively a no-op.
+func warnIfNotIncluded(ctx context.Context, b *bundle.Bundle, filename string) {
+	// b.Config.Include has been overwritten with the expanded list of already
+	// loaded files by ProcessRootIncludes, so re-read the root configuration
+	// file to recover the raw (unexpanded) include patterns.
+	rootFile, err := config.FileNames.FindInPath(b.BundleRootPath)
+	if err != nil {
+		log.Debugf(ctx, "Skipping include check: %v", err)
+		return
+	}
+
+	root, diags := config.Load(rootFile)
+	if diags.HasError() {
+		log.Debugf(ctx, "Skipping include check: failed to load %s: %v", rootFile, diags.Error())
+		return
+	}
+
+	absFilename, err := filepath.Abs(filename)
+	if err != nil {
+		log.Debugf(ctx, "Skipping include check: %v", err)
+		return
+	}
+
+	if isIncluded(b.BundleRootPath, root.Include, absFilename) {
+		return
+	}
+
+	rel, err := filepath.Rel(b.BundleRootPath, absFilename)
+	if err != nil {
+		rel = absFilename
+	}
+	rel = filepath.ToSlash(rel)
+
+	// Suggest a glob that covers the directory the file was written to.
+	suggestion := filepath.ToSlash(filepath.Join(filepath.Dir(rel), "*.yml"))
+
+	logdiag.LogDiag(ctx, diag.Diagnostic{
+		Severity: diag.Warning,
+		Summary:  "Generated configuration is not included in the bundle",
+		Detail: fmt.Sprintf(""+
+			"The file %s is not matched by any pattern in the 'include' section of databricks.yml,\n"+
+			"so it will not be deployed. Add a matching entry to the 'include' section, for example:\n"+
+			"\n"+
+			"include:\n"+
+			"  - %s",
+			rel, suggestion),
+	})
+}
+
+// isIncluded reports whether absFilename is matched by any of the include
+// patterns, resolved the same way as ProcessRootIncludes: each pattern is
+// anchored to the bundle root and expanded with filepath.Glob against the
+// files on disk.
+func isIncluded(bundleRootPath string, include []string, absFilename string) bool {
+	for _, entry := range include {
+		// Includes must be relative paths; the loader errors on absolute ones.
+		if filepath.IsAbs(entry) {
+			continue
+		}
+
+		matches, err := filepath.Glob(filepath.Join(bundleRootPath, entry))
+		if err != nil {
+			continue
+		}
+
+		for _, match := range matches {
+			absMatch, err := filepath.Abs(match)
+			if err != nil {
+				continue
+			}
+			if absMatch == absFilename {
+				return true
+			}
+		}
+	}
+
+	return false
+}
diff --git a/cmd/bundle/generate/include_test.go b/cmd/bundle/generate/include_test.go
new file mode 100644
index 00000000000..74bdd02bcc2
--- /dev/null
+++ b/cmd/bundle/generate/include_test.go
@@ -0,0 +1,66 @@
+package generate
+
+import (
+	"os"
+	"path/filepath"
+	"testing"
+
+	"github.com/stretchr/testify/require"
+)
+
+func TestIsIncluded(t *testing.T) {
+	// Lay out a bundle root with a couple of resource files on disk, because
+	// isIncluded resolves the include patterns with filepath.Glob against the
+	// files that actually exist.
+	root := t.TempDir()
+	included := filepath.Join(root, "resources", "my.job.yml")
+	nested := filepath.Join(root, "resources", "sub", "other.job.yml")
+	for _, f := range []string{included, nested} {
+		require.NoError(t, os.MkdirAll(filepath.Dir(f), 0o755))
+		require.NoError(t, os.WriteFile(f, []byte("{}"), 0o644))
+	}
+
+	tests := []struct {
+		name     string
+		include  []string
+		filename string
+		want     bool
+	}{
+		{
+			name:     "matched by glob",
+			include:  []string{"resources/*.yml"},
+			filename: included,
+			want:     true,
+		},
+		{
+			name:     "not matched, empty include",
+			include:  nil,
+			filename: included,
+			want:     false,
+		},
+		{
+			name:     "glob is not recursive",
+			include:  []string{"resources/*.yml"},
+			filename: nested,
+			want:     false,
+		},
+		{
+			name:     "matched by exact path",
+			include:  []string{"resources/my.job.yml"},
+			filename: included,
+			want:     true,
+		},
+		{
+			name:     "absolute include pattern is ignored",
+			include:  []string{included},
+			filename: included,
+			want:     false,
+		},
+	}
+
+	for _, tt := range tests {
+		t.Run(tt.name, func(t *testing.T) {
+			require.Equal(t, tt.want, isIncluded(root, tt.include, tt.filename))
+		})
+	}
+}
diff --git a/cmd/bundle/generate/job.go b/cmd/bundle/generate/job.go
index c3aba49c5f2..6bb10d30ede 100644
--- a/cmd/bundle/generate/job.go
+++ b/cmd/bundle/generate/job.go
@@ -147,6 +147,8 @@ After generation, you can deploy this job to other targets using:
 
 		cmdio.LogString(ctx, "Job configuration successfully saved to "+filepath.ToSlash(filename))
 
+		warnIfNotIncluded(ctx, b, filename)
+
 		if bind {
 			return deployment.BindResource(cmd, jobKey, strconv.FormatInt(jobId, 10), true, false, true)
 		}
diff --git a/cmd/bundle/generate/pipeline.go b/cmd/bundle/generate/pipeline.go
index 35fb073cadd..cdde5984d40 100644
--- a/cmd/bundle/generate/pipeline.go
+++ b/cmd/bundle/generate/pipeline.go
@@ -151,6 +151,8 @@ like catalogs, schemas, and compute configurations per target.`,
 
 		cmdio.LogString(ctx, "Pipeline configuration successfully saved to "+filepath.ToSlash(filename))
 
+		warnIfNotIncluded(ctx, b, filename)
+
 		if bind {
 			return deployment.BindResource(cmd, pipelineKey, pipelineId, true, false, true)
 		}