diff --git a/README.md b/README.md
index b53068d..5d79c54 100644
--- a/README.md
+++ b/README.md
@@ -56,19 +56,15 @@ file has been configured for
 Integrating with your DeepDive application
 ----
 
-Suppose your app runs in `APP_HOME` and your outputs are saved in `DEEPDIVE_HOME/out`. Suppose you have a `run.sh` script that runs your application, and you want an automatic report each time after `run.sh` finishes:
+Suppose your app runs in `APP_HOME`. Suppose you have a `run.sh` script that runs your application, and you want an automatic report each time after `run.sh` finishes:
 
 Just add into the your `run.sh` a command to run `braindump`. e.g. If your `run.sh` looks like:
 
 ```
 #! /bin/bash
 
-. "$(dirname $0)/env.sh"
-
-cd $DEEPDIVE_HOME
-
 ### Run with deepdive binary:
-deepdive -c $APP_HOME/application.conf
+deepdive run
 ```
 
 Update it to look like this:
@@ -76,18 +72,12 @@ Update it to look like this:
 ```
 #! /bin/bash
 
-. "$(dirname $0)/env.sh"
-
-cd $DEEPDIVE_HOME
-
 # Be sure to set this so that you are able to QUIT if deepdive fails.
 set -e
 
 # Run with deepdive binary:
-deepdive -c $APP_HOME/application.conf
+deepdive run
 
-# Note that you should go back to your APP_HOME directory
-cd $APP_HOME  
 braindump
 ```
 
@@ -103,8 +93,8 @@ APP_HOME/experiment-reports/v00001/:
 ├── calibration                   -- Calibration plots
 │   ├── has_spouse.is_true.png
 │   └── has_spouse.is_true.tsv
-├── code                          -- Saved code for this run (default saves "application.conf" and "udf/")
-│   ├── application.conf
+├── code                          -- Saved code for this run (default saves "deepdive.conf" and "udf/")
+│   ├── deepdive.conf
 │   └── udf
 ├── dd-out                        -- A symbolic link to the corresponding deepdive output directory
 ├── dd-timestamp                  -- A timestamp of this deepdive run
@@ -185,7 +175,7 @@ Configuration Specification
 - `VARIABLE_COLUMNS`: variable columns in the same order of VARIABLE_TABLES. Separated by space. e.g. "v1 v2"
 - `VARIABLE_WORDS_COLUMNS`: if the variable is a mention, specify the words / description for the mention. This is used for a statistics with naive entity linking. If empty (""), do not count deduplicated mentions for that table. Separated by space. e.g. w1 ""
 - `VARIABLE_DOCID_COLUMNS`: specify if there is a field in the variable table that indicates doc_id. This is used to count how many documents have extractions. If empty (""), do not count for that table. Separated by space. e.g. "" did2
-- `CODE_CONFIG`: a config file that specifies what in $APP_HOME to save as codes, one file/folder per line. Default file is saving "application.conf" and "udf".
+- `CODE_CONFIG`: a config file that specifies what in $APP_HOME to save as codes, one file/folder per line. Default file is saving "deepdive.conf" and "udf".
 - `NUM_SAMPLED_FEATURES`: the number of sampled features for each feature table specified in "FEATURE_TABLES"
 - `NUM_SAMPLED_SUPERVISION`: the number of sampled supervision examples for each variable specified in "FEATURE_COLUMNS"
 - `NUM_SAMPLED_RESULT`: the number of sampled inference results for each variable
diff --git a/util/code_default.conf b/util/code_default.conf
index 4d713d4..9c6eaaa 100644
--- a/util/code_default.conf
+++ b/util/code_default.conf
@@ -1,2 +1,2 @@
-application.conf
+deepdive.conf
 udf
diff --git a/util/config-generator/generate.py b/util/config-generator/generate.py
index 65e2616..0f62ed6 100755
--- a/util/config-generator/generate.py
+++ b/util/config-generator/generate.py
@@ -65,9 +65,9 @@
               default='',
               help='specify if there is a field in the variable table that indicates doc_id. This is used to count how many documents have extractions. If empty (""), do not count for that table. Separated by space. e.g. "" did2')
 @click.option('--code_config', 
-              prompt='Specify CODE_CONFIG, a config file that specifies what in $APP_HOME to save as codes, one file/folder per line. Default file is: \napplication.conf\nudf',
+              prompt='Specify CODE_CONFIG, a config file that specifies what in $APP_HOME to save as codes, one file/folder per line. Default file is: \ndeepdive.conf\nudf',
               default='',
-              help='a config file that specifies what in $APP_HOME to save as codes, one file/folder per line. Default file is: \napplication.conf\nudf\n')
+              help='a config file that specifies what in $APP_HOME to save as codes, one file/folder per line. Default file is: \ndeepdive.conf\nudf\n')
 @click.option('--num_sampled_docs', 
               prompt='Specify NUM_SAMPLED_DOCS',
               default='100',
@@ -251,4 +251,4 @@ def generate(output_file,
 
 
 if __name__ == '__main__':
-    generate()
\ No newline at end of file
+    generate()