added configuration docs

Author: emptymalei

docs/tutorials/configuration/index.md

@@ -12,4 +12,45 @@ Run the command
 dataherb configure
 ```
 
-and some questions will show up.
+and some questions will show up:
+
+```bash
+[?] Where should I put all the datasets and flora database? An empty folder is recommended.: ~/dataherb
+[?] How would you name the default flora? Please keep the default value if this is not clear to you.: flora
+```
+
+!!! warning "config file already exists"
+    If a config file (`~/.dataherb/config.json`) is already created, a warning will be shown:
+
+    ```bash
+    Config file (~/.dataherb/config.json) already exists
+    ```
+
+    You could overwrite it or leave it be.
+
+
+
+### Manually Create Configuration
+
+Once the `dataherb configure` command is run, a `config.json` file will be created inside the folder `~/.dataherb`.
+
+```json
+{
+    "workdir": "~/dataherb",
+    "default": {
+        "flora": "flora"
+    }
+}
+```
+
+| key  |  example | description |
+|---|---|---|
+| `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`. |
+
+
+!!! 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`.

mkdocs.yml

@@ -89,3 +89,7 @@ nav:
       - "dataherb.utils.awscli": references/utils/awscli.md
       - "dataherb.utils.data": references/utils/data.md
   - "Changelog": changelog.md
+
+extra_javascript:
+  - 'https://unpkg.com/[email protected]/dist/mermaid.min.js'
+