docs: Restructure documentation and update references

Author: Zhe Yu

.github/workflows/panvimdoc.yml

@@ -15,7 +15,7 @@ jobs:
         uses: kdheepak/panvimdoc@main
         with:
           vimdoc: "VectorCode" # Output vimdoc project name (required)
-          pandoc: "./docs/neovim.md" # Input pandoc file
+          pandoc: "./docs/neovim/README.md" # Input pandoc file
           toc: true # Table of contents
           description: "A code repository indexing tool to supercharge your LLM experience." # Project description used in title (if empty, uses neovim version and current date)
           titledatepattern: "%Y %B %d" # Pattern for the date that used in the title
@@ -32,7 +32,7 @@ jobs:
         uses: kdheepak/panvimdoc@main
         with:
           vimdoc: "VectorCode-cli" # Output vimdoc project name (required)
-          pandoc: "./docs/cli.md" # Input pandoc file
+          pandoc: "./docs/cli/README.md" # Input pandoc file
           toc: true # Table of contents
           description: "A code repository indexing tool to supercharge your LLM experience." # Project description used in title (if empty, uses neovim version and current date)
           titledatepattern: "%Y %B %d" # Pattern for the date that used in the title

README.md

@@ -42,9 +42,9 @@ model output and reduce hallucination.
 > To check for the documentation for the version you're using, you can [check out
 > the corresponding tags](https://github.com/Davidyz/VectorCode/tags).
 
-- For the setup and usage of the command-line tool, see [the CLI documentation](./docs/cli.md);
+- For the setup and usage of the command-line tool, see [the CLI documentation](./docs/cli/README.md);
 - For neovim users, after you've gone through the CLI documentation, please refer to 
-  [the neovim plugin documentation](./docs/neovim.md) for further instructions.
+  [the neovim plugin documentation](./docs/neovim/READMD.md) for further instructions.
 - Additional resources:
   - the [wiki](https://github.com/Davidyz/VectorCode/wiki) for extra tricks and
     tips that will help you get the most out of VectorCode, as well as

docs/cli.md docs/cli/README.mddocs/cli.md renamed to docs/cli/README.md

@@ -125,6 +125,10 @@ A community-maintained Nix package is available
 If you're using nix to install a standalone Chromadb server, make sure to stick
 to [0.6.3](https://github.com/NixOS/nixpkgs/pull/412528).
 
+If you install via Nix and run into an issue, please try to reproduce with the
+PyPi package (install via `uv` or `pipx`). If it's not reproducible on the
+non-nix package, I may close the issue immediately.
+
 ## Getting Started
 
 `cd` into your project root repo, and run:
@@ -305,7 +309,12 @@ The JSON configuration file may hold the following values:
   `CrossEncoderReranker` (default, using 
   [sentence-transformers cross-encoder](https://sbert.net/docs/package_reference/cross_encoder/cross_encoder.html)
   ) and `NaiveReranker` (sort chunks by the "distance" between the embedding
-  vectors);
+  vectors).
+  Note: If you're using a good embedding model (eg. a hosted service from OpenAI, or 
+  a LLM-based embedding model like 
+  [Qwen3-Embedding-0.6B](https://huggingface.co/Qwen/Qwen3-Embedding-0.6B)), you
+  may get better results if you use `NaiveReranker` here because a good embedding
+  model may understand texts better than a mediocre reranking model.
 - `reranker_params`: dictionary, similar to `embedding_params`. The options
   passed to the reranker class constructor. For `CrossEncoderReranker`, these
   are the options passed to the