docs: Update limitation information

README.md

@@ -25,7 +25,9 @@ To check if everything is working you should now see the `extract` command liste
 You will be set up with the default options but if you want to change anything, read on in configuration below.
 
 > **Note**
-> This plugin is still in fairly early development. It does what I need it to do, but if you have a meticulously organized library *please* make backups before doing any operation which could affect your notes, or make use of the papis-included git options.
+> This plugin is still in fairly early development.
+> It does what I need it to do, but if you have a meticulously organized library *please* make backups before doing any operation which could affect your notes, or make use of the papis-included git options.
+> Take care to read the Issues section of this README if you intend to run it over a large collection.
 
 ## Usage
 
@@ -114,8 +116,9 @@ papis extract --template count
 
 For now, these are the only formatters the plugin knows about.
 
-Be aware that if you write to your notes using a different template the plugin will *not* detect old annotations and drop them,
+Be aware that if you re-write to your notes using a completely different template than the original the plugin will *not* detect old annotations and drop them,
 so you will be doubling up your annotations.
+See the `minimum_similarity_color` configuration option for more details.
 
 ## Configuration
 
@@ -150,6 +153,9 @@ if `False` extraction only happens when you explicitly invoke it.
 Extraction will *not* happen automatically when you add new annotations to an existing document,
 regardless of this setting.
 
+> **Note**
+> This option does not work yet due to currently missing upstream features.
+
 ### Automatic tagging
 
 By supplying the tags option with a valid python dictionary of the form `{"tag": "color", "tag2": "color2"}`,
@@ -254,6 +260,7 @@ features to be implemented:
     - called `--template` in current implementation
 - [ ] on_add hook to extract annotations as files are added
     - needs upstream help, 'on_add' hook, and pass-through of affected documents
+- [ ] target same minimum Python version as papis upstream (3.8 as of papis 0.13)
 
 upstream changes:
 
@@ -262,6 +269,12 @@ upstream changes:
 
 ## Issues
 
+First, a note in general: There is the functionality to run this plugin over your whole library in a single command and also in a way that makes permanent changes to that library.
+This is intended and, in my view, an important aspect of what this plugin provides and the batch functionality of cli programs in general.
+However, it can also lead to frustrating clean-up time if something messes up or, in the worst case, data loss.
+The extractors attempt to ascertain what files they can operate on with certain heuristics but will not be fail-safe.
+Take the note at the top of this README to heart and always have backups on hand before larger operations.
+
 A note on the extraction: Highlights in pdfs can be somewhat difficult to parse
 (as are most things in them). Sometimes they contain the selected text that is written on the
 page, sometimes they contain the annotators thoughts as a note, sometimes they contain nothing.