doc: update chef guide

Author: c-dilks

doc/chef_guide.md

@@ -14,22 +14,29 @@ see [the Chefs' documentation wiki](https://clasweb.jlab.org/wiki/index.php/CLAS
 
 Output files will appear in your chosen output directory, within `hist/detectors/`.
 
+> [!NOTE]
+> If you want physics timelines, for now you'll need to use `qtl histogram --focus-physics`; we will eventually include this in the workflow!
+
 ## :green_circle: Step 2: Make the timelines
 
 ```bash
 qtl analysis -d $dataset -i $out_dir/hist/detectors -p $publish_dir
 ```
-- `$out_dir` is your output directory from **Step 1** and `$dataset` is a unique name for this cook, _e.g._, `rga_v1.23`.
+- `$dataset` is a unique name for this cook, _e.g._, `rga_v1.23`
+- `$out_dir` is your output directory from **Step 1**
 - `$publish_dir` is the publishing directory
   - example: `rgb/pass0`
+  - note: the full publishing path will be `/group/clas/www/clas12mon/html/hipo/${publish_dir}/${dataset}`
 
 A URL will be printed upon success, and a link will appear in [`clas12mon`](https://clas12mon.jlab.org/) in your run group's area momentarily.
 
+> [!IMPORTANT]
+> Run `qtl analysis` with no further arguments for additional usage; some options may be _needed_ for your run group!
+
 > [!TIP]
-> Step 2 generates analyzed timeline files and logging information to a
-> separate directory.
+> Step 2 generates analyzed timeline files and logging information to a separate directory.
 > - You can control that directory with the `-o` option, or just use the default.
-> - If using the default, consider making a symbolic link named `outfiles` pointing to somewhere on `/volatile`
+> - If using the default, consider making a symbolic link named `outfiles` pointing to somewhere on `/volatile`, since once timelines are published successfully, you don't really need these output files
 
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