update docs for switching to folder

Author: emptymalei

docs/tutorials/configuration/index.md

@@ -19,6 +19,30 @@ and some questions will show up:
 [?] How would you name the default flora? Please keep the default value if this is not clear to you.: flora
 ```
 
+The first question is setting the workdir.
+
+!!! warning "Different ways of perserving the metadata"
+    We have two different ways of perserving the flora meta data.
+
+    1. Using a single file for all the datasets.
+    2. Using a folder for each dataset.
+
+    `dataherb` supports both. By default, we will use folders. For the above configuration, we will find the folder for all the flora metadata at `~/dataherb/flora/flora`.
+
+    Note that `~/[workdir]/flora/` is the path where we put all the flora metadata. If the answer to the second question, aka name of the flora, is set to `flora2`, we will have all the flora metadata located at `~/[workdir]/flora/flora`2`.
+
+    We can have multiple flora, for example, we can have two, `flora` and `flora2`
+
+    ```bash
+    flora
+    ├── flora
+    │   └── git-dataherb-python-demo-dataset
+    │        └── dataherb.json
+    └── flora2
+        └── git-dataherb-python-demo-dataset-2
+            └── dataherb.json
+    ```
+
 !!! warning "config file already exists"
     If a config file (`~/.dataherb/config.json`) is already created, a warning will be shown:
 
@@ -67,7 +91,8 @@ Once the `dataherb configure` command is run, a `config.json` file will be creat
 {
     "workdir": "~/dataherb",
     "default": {
-        "flora": "flora"
+        "flora": "flora",
+        "aggregrated": false
     }
 }
 ```
@@ -76,10 +101,11 @@ Once the `dataherb configure` command is run, a `config.json` file will be creat
 |---|---|---|
 | `workdir`  |  `~/dataherb` | The work directory for dataherb. |
 | `default.flora`  | `flora` |  The name of the flora to be used by default. For example, the value `flora` means we will use the `flora.json` database in the folder `(workdir setting in the above row)/flora/flora.json`. |
+| `default.aggregrated`  | `false` |  Whether to use a single json file for all the flora metadata. It is highly recommended to set it to `false`. |
 
 
 !!! note "More about `workdir`"
     By default, two folders will be created inside it: `~/dataherb/flora` (default storage for all flora) and `~/dataherb/serve` (the cache folder for the website of all datasets when we run `dataherb serve`)
 
 !!! note "More about `default.flora`"
-    If `workdir` is set to `~/dataherb`, then the database will be `~/dataherb/flora/flora.json`. If the value of `default.flora` is set to `abc`, then the database will be `~/dataherb/flora/abc.json`.
+    If `workdir` is set to `~/dataherb`, then the database will be `~/dataherb/flora/flora`. If the value of `default.flora` is set to `abc`, then the database will be `~/dataherb/flora/abc`.