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docs: Improved and updated wiki docs on RAGs

Dark-Alex-17
2026-08-12 13:05:40 -06:00
parent ee8b5781be
commit f03d49ea65
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Agents.md
+1 -1
@@ -310,7 +310,7 @@ of documents that Coyote supports and how to use custom document loaders, refer
Anytime your agent starts up, it will automatically be using the RAG you've defined here. Anytime your agent starts up, it will automatically be using the RAG you've defined here.
The first time an agent starts with documents attached, Coyote offers to build the knowledge base and asks which The first time an agent starts with documents attached, Coyote offers to build the knowledge base and asks which
[storage driver](RAG#storage-drivers) to store it with — `yaml` (the default, and what Coyote has always done) or [storage driver](RAG#storage-drivers) to store it with. `yaml` (the default, and what Coyote has always done) or
`duckdb`, which keeps the vectors and text on disk so a large corpus doesn't have to be read back into memory on every `duckdb`, which keeps the vectors and text on disk so a large corpus doesn't have to be read back into memory on every
start. The choice is fixed once the knowledge base is built: changing it means removing the agent's built knowledge start. The choice is fixed once the knowledge base is built: changing it means removing the agent's built knowledge
base and letting it rebuild, which re-embeds every document. base and letting it rebuild, which re-embeds every document.
Graph-Agents.md
+2 -2
@@ -585,12 +585,12 @@ base is first built):
(default: `1`). `0` returns only documents directly linked to matched entities with no traversal. (default: `1`). `0` returns only documents directly linked to matched entities with no traversal.
Falls back to `rag_graph_hops`. Higher values surface more loosely related documents; keep at `1` for most corpora. Falls back to `rag_graph_hops`. Higher values surface more loosely related documents; keep at `1` for most corpora.
- **`batch_size`:** Embedding-request batch size. - **`batch_size`:** Embedding-request batch size.
- **`driver`:** [Storage driver](RAG#storage-drivers) for this node's knowledge base — `yaml` - **`driver`:** [Storage driver](RAG#storage-drivers) for this node's knowledge base. Can be `yaml`
(default) or `duckdb`. Use `duckdb` when the node's corpus is large enough that rebuilding (default) or `duckdb`. Use `duckdb` when the node's corpus is large enough that rebuilding
the in-memory index on every agent start is noticeable; it keeps vectors and text on disk in the in-memory index on every agent start is noticeable; it keeps vectors and text on disk in
a `<rag-node-id>.duckdb` file beside the generated knowledge base. An invalid driver is a `<rag-node-id>.duckdb` file beside the generated knowledge base. An invalid driver is
rejected when the graph is validated, naming the offending node. Like every field in this rejected when the graph is validated, naming the offending node. Like every field in this
section it only applies when the knowledge base is *first* built — changing it later has no section, it only applies when the knowledge base is *first* built. Changing it later has no
effect until the knowledge base is deleted and rebuilt. When the node omits it and the knowledge effect until the knowledge base is deleted and rebuilt. When the node omits it and the knowledge
base is built interactively, Coyote asks which driver to use; setting it here answers that base is built interactively, Coyote asks which driver to use; setting it here answers that
question up front. The `qdrant` driver is not available here: attaching a remote collection is an question up front. The `qdrant` driver is not available here: attaching a remote collection is an
RAG.md
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@@ -69,14 +69,14 @@ When you define RAG, Coyote will first "build" the RAG. This means that Coyote w
generate [embeddings](https://huggingface.co/spaces/hesamation/primer-llm-embedding) for that text. This essentially just means that Coyote translates the document into a language generate [embeddings](https://huggingface.co/spaces/hesamation/primer-llm-embedding) for that text. This essentially just means that Coyote translates the document into a language
the LLM can understand. the LLM can understand.
These embeddings are stored in a vector database — in memory, on disk, or in a remote Qdrant collection, depending on These embeddings are stored in a vector database. It is either in memory, on disk, or in a remote Qdrant collection,
the RAG's [storage driver](#storage-drivers). Coyote also indexes every document chunk in a full-text depending on the RAG's [storage driver](#storage-drivers). Coyote also indexes every document chunk in a full-text
search index (BM25) for keyword-based retrieval. search index (BM25) for keyword-based retrieval.
Building costs real time and real money: every chunk is sent to an embedding model, and every chunk is sent again to a Building costs real time and real money: every chunk is sent to an embedding model, and every chunk is sent again to a
chat model if graph RAG is enabled. Adding or editing documents with `.edit rag-docs` only processes what actually chat model if graph RAG is enabled. Adding or editing documents with `.edit rag-docs` only processes what actually
changed, but `.rebuild rag` deliberately re-embeds the entire corpus from scratch — reach for it when a document's changed, but `.rebuild rag` deliberately re-embeds the entire corpus from scratch. You should only reach for it when a
contents changed underneath Coyote or the knowledge base looks wrong, not as routine maintenance. document's contents changed underneath Coyote or the knowledge base looks wrong, not as routine maintenance.
If an [extractor model is configured](#graph-based-rag), Coyote additionally runs an LLM-based entity and relationship If an [extractor model is configured](#graph-based-rag), Coyote additionally runs an LLM-based entity and relationship
extraction pass over each document chunk and builds a **knowledge graph** of named entities and their connections. This extraction pass over each document chunk and builds a **knowledge graph** of named entities and their connections. This
@@ -124,13 +124,13 @@ giving the model query-specific context to answer your question.
Every RAG picks a **storage driver** when it's created. The driver decides where your vectors and document text Every RAG picks a **storage driver** when it's created. The driver decides where your vectors and document text
actually live: inside the RAG's own file, in a local database beside it, or in a Qdrant server you already run. actually live: inside the RAG's own file, in a local database beside it, or in a Qdrant server you already run.
| Driver | Where the vectors live | Reach for it when | | Driver | Where the vectors live | Reach for it when |
|--------|------------------------|-------------------| |--------------------|-------------------------------------------------------|-----------------------------------------------------------------------------------------------|
| `yaml` *(default)* | In the RAG's own YAML file, loaded into memory on use | You want the simplest thing that works, or several Coyote processes need the same RAG at once | | `yaml` *(default)* | In the RAG's own YAML file, loaded into memory on use | You want the simplest thing that works, or several Coyote processes need the same RAG at once |
| `duckdb` | A `<name>.duckdb` file beside the RAG | The corpus is large enough that re-loading it into memory on every start is annoying | | `duckdb` | A `<name>.duckdb` file beside the RAG | The corpus is large enough that re-loading it into memory on every start is annoying |
| `qdrant` | A collection on a Qdrant server you already run | Something else already built and maintains the collection | | `qdrant` | A collection on a Qdrant server you already run | Something else already built and maintains the collection |
Coyote asks which one you want whenever it builds a knowledge base interactively — creating a RAG with `.rag`, an Coyote asks which one you want whenever it builds a knowledge base interactively, creating a RAG with `.rag`, an
[agent](Agents#3-initializing-rag) starting up for the first time, or a [graph agent's](Graph-Agents) `rag` node: [agent](Agents#3-initializing-rag) starting up for the first time, or a [graph agent's](Graph-Agents) `rag` node:
```text ```text
@@ -141,7 +141,7 @@ Coyote asks which one you want whenever it builds a knowledge base interactively
If you don't care, take the default. `yaml` is what Coyote has always done. If you don't care, take the default. `yaml` is what Coyote has always done.
> **A RAG's driver is fixed when it's created.** There is no conversion step — switching means deleting the RAG and > **A RAG's driver is fixed when it's created.** There is no conversion step. Switching means deleting the RAG and
> building it again, which re-embeds every document. Worth a moment's thought before you pick, but not worth agonizing > building it again, which re-embeds every document. Worth a moment's thought before you pick, but not worth agonizing
> over: for small corpora the difference is not something you'll notice. > over: for small corpora the difference is not something you'll notice.
@@ -150,7 +150,7 @@ The default. Vectors and document text are stored in the RAG's YAML file and rea
where the HNSW index is built on the fly. where the HNSW index is built on the fly.
Its useful property is that nothing holds a lock: as many Coyote processes as you like can use the same RAG Its useful property is that nothing holds a lock: as many Coyote processes as you like can use the same RAG
simultaneously. Its cost is startup — a large corpus means a large file to parse every time the RAG is loaded. simultaneously. Its cost is startup: a large corpus means a large file to parse every time the RAG is loaded.
## duckdb ## duckdb
Vectors, document text and the search indexes live in a `<name>.duckdb` file next to the RAG, and stay there between Vectors, document text and the search indexes live in a `<name>.duckdb` file next to the RAG, and stay there between
@@ -164,22 +164,22 @@ Two things are worth knowing before you choose it:
* **First use needs network access.** DuckDB's vector (`vss`) and full-text (`fts`) extensions are downloaded the * **First use needs network access.** DuckDB's vector (`vss`) and full-text (`fts`) extensions are downloaded the
first time a duckdb RAG is created, then cached and reused. On a machine that's offline from the start, create one first time a duckdb RAG is created, then cached and reused. On a machine that's offline from the start, create one
duckdb RAG while connected and every later one works offline. Pre-installing them from a DuckDB shell is fiddlier duckdb RAG while connected and every later one works offline. Pre-installing them from a DuckDB shell is fiddlier
than it sounds — the cache is keyed by DuckDB version, and Coyote bundles its own — so connecting once is much the than it sounds (the cache is keyed by DuckDB version, and Coyote bundles its own), so connecting once is much the
easier route. easier route.
Deleting the RAG removes the `.duckdb` file and its write-ahead log along with it. Deleting the RAG removes the `.duckdb` file and its write-ahead log along with it.
A duckdb RAG is **two files**: the `<name>.yaml` and the `<name>.duckdb` beside it. Copy, move or back up both A duckdb RAG is **two files**: the `<name>.yaml` and the `<name>.duckdb` beside it. Copy, move or back up both
together. The YAML deliberately holds no vectors, so a RAG that arrives without its store loads without complaint, together. The YAML deliberately holds no vectors, so a RAG that arrives without its store loads without complaint,
still lists every indexed document, and answers every query with nothing. Coyote warns when it sees that combination — still lists every indexed document, and answers every query with nothing. Coyote warns when it sees that combination
indexed files, empty store — naming the file it expected. If the store is genuinely gone, `.rebuild rag` re-embeds the (i.e. indexed files, empty store) naming the file it expected. If the store is genuinely gone, `.rebuild rag` re-embeds
corpus from scratch; `.edit rag-docs` will *not* refill it, because unchanged documents are skipped by hash. the corpus from scratch; `.edit rag-docs` will *not* refill it, because unchanged documents are skipped by hash.
## qdrant — attaching an existing collection ## qdrant - attaching an existing collection
The `qdrant` driver connects a RAG to a collection on a Qdrant server you already run. It is **read-only**: Coyote The `qdrant` driver connects a RAG to a collection on a Qdrant server you already run. It is **read-only**: Coyote
queries the collection and never writes to it, so whatever populated it stays the sole owner of its contents. This is queries the collection and never writes to it, so whatever populated it stays the sole owner of its contents. This is
the driver to use when another system — a LangChain pipeline, an ingestion job, a colleague's tooling — already the driver to use when another system, be that a LangChain pipeline, an ingestion job, a colleague's tooling, etc., and
maintains a collection you'd like to ask questions about. it already maintains a collection you'd like to ask questions about.
Because the collection already exists, you don't create this kind of RAG with `.rag`; you *attach* it: Because the collection already exists, you don't create this kind of RAG with `.rag`; you *attach* it:
@@ -189,13 +189,13 @@ Because the collection already exists, you don't create this kind of RAG with `.
Coyote then walks you through it: Coyote then walks you through it:
1. **Host** — for example `qdrant.company.com:6333`. 1. **Host:** For example `qdrant.company.com:6333`.
2. **API key** — Coyote asks whether the instance needs one, then which [Vault](Vault) secret holds it (defaulting to 2. **API key:** Coyote asks whether the instance needs one, then which [Vault](Vault) secret holds it (defaulting to
`QDRANT_API_KEY`). If that secret doesn't exist yet you can create it right there, without leaving the wizard. The `QDRANT_API_KEY`). If that secret doesn't exist yet you can create it right there, without leaving the wizard. The
key itself is never written into the RAG file; only the secret's name is. key itself is never written into the RAG file; only the secret's name is.
3. **Collection** — Coyote connects, lists what's available, and lets you pick. 3. **Collection:** Coyote connects, lists what's available, and lets you pick.
It then checks the collection is actually usable and tells you what it found — the vector dimension, and a warning if It then checks the collection is actually usable and tells you what it found: the vector dimension, and a warning if
the collection is empty (you can attach anyway, but every query will return nothing until something writes to it). the collection is empty (you can attach anyway, but every query will return nothing until something writes to it).
A collection has to meet two requirements: A collection has to meet two requirements:
@@ -208,11 +208,11 @@ A collection has to meet two requirements:
Point IDs may be integers or UUIDs; both work. Point IDs may be integers or UUIDs; both work.
> **A Qdrant on your own machine or network is contacted directly.** If `HTTP_PROXY` or `HTTPS_PROXY` are set in your > **A Qdrant on your own machine or network is contacted directly.** If `HTTP_PROXY` or `HTTPS_PROXY` are set in your
> environment, Coyote still reaches a loopback, private-range or `.local` host without going through the proxy — a > environment, Coyote still reaches a loopback, private-range or `.local` host without going through the proxy. A
> proxy that has never heard of your local server would otherwise refuse the connection outright. A remote Qdrant > proxy that has never heard of your local server would otherwise refuse the connection outright. A remote Qdrant
> continues to honour whatever your environment configures. > continues to honour whatever your environment configures.
> **Use the same embedding model that built the collection.** Coyote can't detect a mismatch — the dimensions may line > **Use the same embedding model that built the collection.** Coyote can't detect a mismatch. The dimensions may line
> up perfectly while the vectors mean entirely different things. The symptom is retrieval that returns confident > up perfectly while the vectors mean entirely different things. The symptom is retrieval that returns confident
> nonsense, so it's worth checking rather than discovering later. > nonsense, so it's worth checking rather than discovering later.
@@ -224,15 +224,15 @@ sbx proxy automatically, so queries work inside the sandbox exactly as they do o
# Supported Document Sources # Supported Document Sources
Coyote supports a number of document sources that can be used for RAG: Coyote supports a number of document sources that can be used for RAG:
| Source | Example | Comments | | Source | Example | Comments |
|--------------------------|-----------------------------------------------------------------------|----------------------------------------------------------------------------------------------------------------------------------------------------------| |--------------------------|-----------------------------------------------------------------------|----------------------------------------------------------------------------------------------------------------------------------------------------------------|
| Files | `/tmp/dir1/file1;/tmp/dir1/file2` | | | Files | `/tmp/dir1/file1;/tmp/dir1/file2` | |
| Directory | `/tmp/dir` | Picks up all files in a directory and all its subdirectories | | Directory | `/tmp/dir` | Picks up all files in a directory and all its subdirectories |
| Directory (extensions} | `/tmp/dir2/**/*.{md,txt}` | Finds all files in all subdirectories with the specified extensions | | Directory (extensions} | `/tmp/dir2/**/*.{md,txt}` | Finds all files in all subdirectories with the specified extensions |
| Recursive Filename | `/tmp/*/COYOTE.md` | The following files will be picked up: <br><ul><li>`/tmp/dir1/COYOTE.md`</li><li>`/tmp/dir2/subdir1/COYOTE.md`</li><li>`/tmp/dir2/subdir2/COYOTE.md`</li></ul> | | Recursive Filename | `/tmp/*/COYOTE.md` | The following files will be picked up: <br><ul><li>`/tmp/dir1/COYOTE.md`</li><li>`/tmp/dir2/subdir1/COYOTE.md`</li><li>`/tmp/dir2/subdir2/COYOTE.md`</li></ul> |
| URL | `https://www.ohdsi.org/data-standardization/` | Downloads and loads the specified webpage into the <br>knowledge base | | URL | `https://www.ohdsi.org/data-standardization/` | Downloads and loads the specified webpage into the <br>knowledge base |
| Recursive URL (Websites) | `https://github.com/OHDSI/Vocabulary-v5.0/wiki/**` | Crawls all pages under the given URL and loads them <br>into the knowledge base | | Recursive URL (Websites) | `https://github.com/OHDSI/Vocabulary-v5.0/wiki/**` | Crawls all pages under the given URL and loads them <br>into the knowledge base |
| Document Loader (custom) | `jina:https://cloud.google.com/bigquery/docs/reference/standard-sql/` | Use a custom document loader to parse the given document | | Document Loader (custom) | `jina:https://cloud.google.com/bigquery/docs/reference/standard-sql/` | Use a custom document loader to parse the given document |
# Document Loaders # Document Loaders
Coyote only has built-in support for loading text files. But that functionality can be extended to read all kinds of files Coyote only has built-in support for loading text files. But that functionality can be extended to read all kinds of files
REPL.md
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@@ -145,15 +145,15 @@ For more information, see the [Todo System documentation](TODO-System).
RAG (Retrieval Augmented Generation) enables you to load documents into the LLM so you can ask questions about it or RAG (Retrieval Augmented Generation) enables you to load documents into the LLM so you can ask questions about it or
complete tasks using the documents as additional context. complete tasks using the documents as additional context.
| Command | Description | | Command | Description |
|------------------|------------------------------------------------------------------------------| |----------------------|-------------------------------------------------------------------------------------------------------------------|
| `.rag` | Initialize or access a RAG | | `.rag` | Initialize or access a RAG |
| `.rag attach <name>` | Attach a RAG to an existing remote [Qdrant](RAG#qdrant--attaching-an-existing-collection) collection (read-only) | | `.rag attach <name>` | Attach a RAG to an existing remote [Qdrant](RAG#qdrant---attaching-an-existing-collection) collection (read-only) |
| `.edit rag-docs` | Add or remove documents from the active RAG using your preferred text editor | | `.edit rag-docs` | Add or remove documents from the active RAG using your preferred text editor |
| `.rebuild rag` | Rebuild the active RAG from scratch, re-embedding every document | | `.rebuild rag` | Rebuild the active RAG from scratch, re-embedding every document |
| `.sources rag` | Show a works-cited of the sources used in the last query | | `.sources rag` | Show a works-cited of the sources used in the last query |
| `.info rag` | Display information about the active RAG | | `.info rag` | Display information about the active RAG |
| `.exit rag` | Exit the active RAG | | `.exit rag` | Exit the active RAG |
![rag](./images/rag/persistent-rag.gif) ![rag](./images/rag/persistent-rag.gif)
Sandboxes.md
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@@ -189,7 +189,7 @@ network policy, and the API key has to reach the server without ever entering th
When you attach a RAG, Coyote writes a small mixin next to it declaring the host as an allowed domain and the API key When you attach a RAG, Coyote writes a small mixin next to it declaring the host as an allowed domain and the API key
as a proxy-managed credential. On launch that mixin is discovered alongside the generated `coyote-mcp` one, the key is as a proxy-managed credential. On launch that mixin is discovered alongside the generated `coyote-mcp` one, the key is
registered with the sbx secret store on your host, and the proxy writes it into the outgoing request header at the registered with the sbx secret store on your host, and the proxy writes it into the outgoing request header at the
network edge — the same treatment LLM provider keys get. Queries then behave identically inside and outside the network edge (the same treatment LLM provider keys get). Queries then behave identically inside and outside the
sandbox. sandbox.
This is also why a RAG's `api_key` must be a `{{SECRET_NAME}}` placeholder rather than the key itself: Coyote reads This is also why a RAG's `api_key` must be a `{{SECRET_NAME}}` placeholder rather than the key itself: Coyote reads