chore: bump Cargo.toml to 0.2.0

CHANGELOG.md

@@ -1,3 +1,34 @@
+## v0.2.0 (2026-02-14)
+
+### Feat
+
+- Simplified sisyphus prompt to improve functionality
+- Supported the injection of RAG sources into the prompt, not just via the `.sources rag` command in the REPL so models can directly reference the documents that supported their responses
+- Created the Sisyphus agent to make Loki function like Claude Code, Gemini, Codex, etc.
+- Created the Oracle agent to handle high-level architectural decisions and design questions about a given codebase
+- Updated the coder agent to be much more task-focused and to be delegated to by Sisyphus
+- Created the explore agent for exploring codebases to help answer questions
+- Use the official atlassian MCP server for the jira-helper agent
+- Created fs_glob to enable more targeted file exploration utilities
+- Created a new tool 'fs_grep' to search a given file's contents for relevant lines to reduce token usage for smaller models
+- Created the new fs_read tool to enable controlled reading of a file
+- Let agent level variables be defined to bypass guard protections for tool invocations
+- Implemented a built-in task management system to help smaller LLMs complete larger multistep tasks and minimize context drift
+- Improved tool and MCP invocation error handling by returning stderr to the model when it is available
+- Added variable interpolation for conversation starters in agents
+- Implemented retry logic for failed tool invocations so the LLM can learn from the result and try again; Also implemented chain loop detection to prevent loops
+- Added gemini-3-pro to the supported vertexai models
+- Added an environment variable that lets users bypass guard operations in bash scripts. This is useful for agent routing
+- Added support for thought-signatures for Gemini 3+ models
+
+### Fix
+
+- Improved continuation prompt to not make broad todo-items
+- Allow auto-continuation to work in agents after a session is compressed and if there's still unfinish items in the to-do list
+- fs_ls and fs_cat outputs should always redirect to "$LLM_OUTPUT" including on errors.
+- Claude tool calls work incorrectly when tool doesn't require any arguments or flags; would provide an empty JSON object or error on no args
+- Fixed a bug where --agent-variable values were not being passed to the agents
+
 ## v0.1.3 (2025-12-13)
 
 ### Feat

Cargo.toml

@@ -1,6 +1,6 @@
 [package]
 name = "loki-ai"
-version = "0.1.3"
+version = "0.2.0"
 edition = "2024"
 authors = ["Alex Clarke <alex.j.tusa@gmail.com>"]
 description = "An all-in-one, batteries included LLM CLI Tool"

assets/agents/sisyphus/config.yaml

@@ -116,68 +116,23 @@ instructions: |
 
   User: "Add a new API endpoint for user profiles"
 
-  ```
-  1. start_task --goal "Add user profiles API endpoint"
-  2. todo__init --goal "Add user profiles API endpoint"
-  3. todo__add --task "Explore existing API patterns and code conventions"
-  4. todo__add --task "Implement profile endpoint"
-  5. todo__add --task "Verify implementation with build/test"
-  6. todo__add --task "Write/update tests for new/updated code (if necessary)"
-  7. todo__add --task "Verify tests pass"
-  8. todo__add --task "Clean-up code and clear any linter warnings"
-  9. todo__add --task "Verify clean-up with build/test"
-  10. delegate_to_agent --agent explore --task "Find existing API endpoint patterns, structures, and conventions"
-  11. todo__done --id 1
-  11. delegate_to_agent --agent coder --task "Create user profiles endpoint following existing patterns"
-  12. todo__done --id 2
-  13. run_build
-  14. run_tests
-  15. todo__done --id 3
-  16. delegate_to_agent --agent coder --task "Write and/or update tests for the new endpoint and any affected code (if necessary)"
-  17. todo__done --id 4
-  18. run_tests
-  19. todo__done --id 5
-  20. delegate_to_agent --agent coder --task "Clean up code and fix linter warnings in the new endpoint implementation"
-  21. todo__done --id 6
-  22. run_build
-  23. run_tests
-  24. todo__done --id 7
-  25. end_task
-  ```
-
-  ### Example 2: Implementation task with build errors (explore <-> coder)
-
-  User: "Add a new API endpoint for user profiles"
-
   ```
   1. start_task --goal "Add user profiles API endpoint"
   2. todo__init --goal "Add user profiles API endpoint"
   3. todo__add --task "Explore existing API patterns"
   4. todo__add --task "Implement profile endpoint"
-  5. todo__add --task "Verify implementation with build/test"
-  6. todo__add --task "Clean-up code and clear any linter warnings"
-  7. todo__add --task "Verify clean-up with build/test"
-  8. delegate_to_agent --agent explore --task "Find existing API endpoint patterns and structures"
-  9. todo__done --id 1
-  10. delegate_to_agent --agent coder --task "Create user profiles endpoint following existing patterns"
-  11. todo__done --id 2
-  12. run_build
-  13. todo__add --task "Fix compilation errors"
-  14. todo__add --task "Verify fixes with build/test"
-  15. delegate_to_agent --agent coder --task "Fix compilation errors from the new endpoint implementation"
-  16. todo__done --id 5
-  17. run_build
-  18. run_tests
-  19. todo__done --id 6
-  20. todo__done --id 3
-  21. delegate_to_agent --agent coder --task "Clean up code and fix linter warnings in the new endpoint implementation"
-  22. todo__done --id 4
-  23. run_build
-  24. run_tests
-  25. todo__done --id 7
+  5. todo__add --task "Verify with build/test"
+  6. delegate_to_agent --agent explore --task "Find existing API endpoint patterns and structures"
+  7. todo__done --id 1
+  8. delegate_to_agent --agent coder --task "Create user profiles endpoint following existing patterns"
+  9. todo__done --id 2
+  10. run_build
+  11. run_tests
+  12. todo__done --id 3
+  13. end_task
   ```
 
-  ### Example 3: Architecture/design question (explore -> oracle)
+  ### Example 2: Architecture/design question (explore -> oracle)
 
   User: "How should I structure the authentication for this app?"
 
@@ -193,7 +148,7 @@ instructions: |
   9. end_task
   ```
 
-  ### Example 4: Vague/open-ended question (oracle directly)
+  ### Example 3: Vague/open-ended question (oracle directly)
 
   User: "What do you think of this codebase structure?"
 

config.example.yaml

@@ -41,7 +41,7 @@ vault_password_file: null        # Path to a file containing the password for th
 # See the [Tools documentation](./docs/function-calling/TOOLS.md) for more details
 function_calling: true           # Enables or disables function calling (Globally).
 mapping_tools:                   # Alias for a tool or toolset
-  fs: 'fs_cat,fs_ls,fs_mkdir,fs_rm,fs_write'
+  fs: 'fs_cat,fs_ls,fs_mkdir,fs_rm,fs_write,fs_read,fs_glob,fs_grep'
 enabled_tools: null              # Which tools to enable by default. (e.g. 'fs,web_search_loki')
 visible_tools:                   # Which tools are visible to be compiled (and are thus able to be defined in 'enabled_tools')
 #  - demo_py.py
@@ -53,6 +53,9 @@ visible_tools:                   # Which tools are visible to be compiled (and a
 #  - fetch_url_via_jina.sh
   - fs_cat.sh
   - fs_ls.sh
+#  - fs_read.sh
+#  - fs_glob.sh
+#  - fs_grep.sh
 #  - fs_mkdir.sh
 #  - fs_patch.sh
 #  - fs_write.sh
@@ -92,7 +95,7 @@ rag_reranker_model: null         # Specifies the reranker model used for sorting
 rag_top_k: 5                     # Specifies the number of documents to retrieve for answering queries
 rag_chunk_size: null             # Defines the size of chunks for document processing in characters
 rag_chunk_overlap: null          # Defines the overlap between chunks
-# Defines the query structure using variables like __CONTEXT__ and __INPUT__ to tailor searches to specific needs
+# Defines the query structure using variables like __CONTEXT__, __SOURCES__, and __INPUT__ to tailor searches to specific needs
 rag_template: |
   Answer the query based on the context while respecting the rules. (user query, some textual context and rules, all inside xml tags)
 
@@ -100,6 +103,10 @@ rag_template: |
   __CONTEXT__
   </context>
 
+  <sources>
+  __SOURCES__
+  </sources>
+
   <rules>
   - If you don't know, just say so.
   - If you are not sure, ask for clarification.
@@ -107,6 +114,7 @@ rag_template: |
   - If the context appears unreadable or of poor quality, tell the user then answer as best as you can.
   - If the answer is not in the context but you think you know the answer, explain that to the user then answer with your own knowledge.
   - Answer directly and without using xml tags.
+  - When using information from the context, cite the relevant source from the <sources> section.
   </rules>
 
   <user_query>

docs/RAG.md

@@ -265,12 +265,14 @@ When you use RAG in Loki, after Loki performs the lookup for relevant chunks of
 will add the retrieved text chunks as context to your query before sending it to the model. The format of this context
 is determined by the `rag_template` setting in your global Loki configuration file.
 
-This template utilizes two placeholders:
+This template utilizes three placeholders:
 * `__INPUT__`: The user's actual query
 * `__CONTEXT__`: The context retrieved from RAG
+* `__SOURCES__`: A numbered list of the source file paths or URLs that the retrieved context came from
 
 These placeholders are replaced with the corresponding values into the template and make up what's actually passed to 
-the model at query-time.
+the model at query-time. The `__SOURCES__` placeholder enables the model to cite which documents its answer is based on,
+which is especially useful when building knowledge-base assistants that need to provide verifiable references.
 
 The default template that Loki uses is the following:
 
@@ -281,6 +283,10 @@ Answer the query based on the context while respecting the rules. (user query, s
 __CONTEXT__
 </context>
 
+<sources>
+__SOURCES__
+</sources>
+
 <rules>
 - If you don't know, just say so.
 - If you are not sure, ask for clarification.
@@ -288,6 +294,7 @@ __CONTEXT__
 - If the context appears unreadable or of poor quality, tell the user then answer as best as you can.
 - If the answer is not in the context but you think you know the answer, explain that to the user then answer with your own knowledge.
 - Answer directly and without using xml tags.
+- When using information from the context, cite the relevant source from the <sources> section.
 </rules>
 
 <user_query>
@@ -296,4 +303,5 @@ __INPUT__
 ```
 
 You can customize this template by specifying the `rag_template` setting in your global Loki configuration file. Your 
-template *must* include both the `__INPUT__` and `__CONTEXT__` placeholders in order for it to be valid.
+template *must* include both the `__INPUT__` and `__CONTEXT__` placeholders in order for it to be valid. The 
+`__SOURCES__` placeholder is optional. If it is omitted, source references will not be included in the prompt.

docs/function-calling/TOOLS.md

@@ -38,6 +38,9 @@ be enabled/disabled can be found in the [Configuration](#configuration) section
 | [`fetch_url_via_curl.sh`](../../assets/functions/tools/fetch_url_via_curl.sh)       | Extract the content from a given URL using cURL.                                                                                                                                                                                     | 🔴               |
 | [`fetch_url_via_jina.sh`](../../assets/functions/tools/fetch_url_via_jina.sh)       | Extract the content from a given URL using Jina.                                                                                                                                                                                     | 🔴               |
 | [`fs_cat.sh`](../../assets/functions/tools/fs_cat.sh)                               | Read the contents of a file at the specified path.                                                                                                                                                                                   | 🟢               |
+| [`fs_read.sh`](../../assets/functions/tools/fs_read.sh)                             | Controlled reading of the contents of a file at the specified path  with line numbers, offset, and limit to read specific sections.                                                                                                  | 🟢               |
+| [`fs_glob.sh`](../../assets/functions/tools/fs_glob.sh)                             | Find files by glob pattern. Returns matching file paths sorted by modification time.                                                                                                                                                 | 🟢               |
+| [`fs_grep.sh`](../../assets/functions/tools/fs_grep.sh)                             | Search file contents using regular expressions. Returns matching file paths and lines.                                                                                                                                               | 🟢               |
 | [`fs_ls.sh`](../../assets/functions/tools/fs_ls.sh)                                 | List all files and directories at the specified path.                                                                                                                                                                                | 🟢               |
 | [`fs_mkdir.sh`](../../assets/functions/tools/fs_mkdir.sh)                           | Create a new directory at the specified path.                                                                                                                                                                                        | 🔴               |
 | [`fs_patch.sh`](../../assets/functions/tools/fs_patch.sh)                           | Apply a patch to a file at the specified path. <br>This can be used to edit a file without having to rewrite the whole file.                                                                                                         | 🔴               |

src/config/mod.rs

@@ -96,6 +96,10 @@ const RAG_TEMPLATE: &str = r#"Answer the query based on the context while respec
 __CONTEXT__
 </context>
 
+<sources>
+__SOURCES__
+</sources>
+
 <rules>
 - If you don't know, just say so.
 - If you are not sure, ask for clarification.
@@ -103,6 +107,7 @@ __CONTEXT__
 - If the context appears unreadable or of poor quality, tell the user then answer as best as you can.
 - If the answer is not in the context but you think you know the answer, explain that to the user then answer with your own knowledge.
 - Answer directly and without using xml tags.
+- When using information from the context, cite the relevant source from the <sources> section.
 </rules>
 
 <user_query>
@@ -1756,10 +1761,10 @@ impl Config {
         abort_signal: AbortSignal,
     ) -> Result<String> {
         let (reranker_model, top_k) = rag.get_config();
-        let (embeddings, ids) = rag
+        let (embeddings, sources, ids) = rag
             .search(text, top_k, reranker_model.as_deref(), abort_signal)
             .await?;
-        let text = config.read().rag_template(&embeddings, text);
+        let text = config.read().rag_template(&embeddings, &sources, text);
         rag.set_last_sources(&ids);
         Ok(text)
     }
@@ -1781,7 +1786,7 @@ impl Config {
         }
     }
 
-    pub fn rag_template(&self, embeddings: &str, text: &str) -> String {
+    pub fn rag_template(&self, embeddings: &str, sources: &str, text: &str) -> String {
         if embeddings.is_empty() {
             return text.to_string();
         }
@@ -1789,6 +1794,7 @@ impl Config {
             .as_deref()
             .unwrap_or(RAG_TEMPLATE)
             .replace("__CONTEXT__", embeddings)
+            .replace("__SOURCES__", sources)
             .replace("__INPUT__", text)
     }
 

src/rag/mod.rs

@@ -298,16 +298,48 @@ impl Rag {
         top_k: usize,
         rerank_model: Option<&str>,
         abort_signal: AbortSignal,
-    ) -> Result<(String, Vec<DocumentId>)> {
+    ) -> Result<(String, String, Vec<DocumentId>)> {
         let ret = abortable_run_with_spinner(
             self.hybird_search(text, top_k, rerank_model),
             "Searching",
             abort_signal,
         )
         .await;
-        let (ids, documents): (Vec<_>, Vec<_>) = ret?.into_iter().unzip();
-        let embeddings = documents.join("\n\n");
-        Ok((embeddings, ids))
+        let results = ret?;
+        let ids: Vec<_> = results.iter().map(|(id, _)| *id).collect();
+        let embeddings = results
+            .iter()
+            .map(|(id, content)| {
+                let source = self.resolve_source(id);
+                format!("[Source: {source}]\n{content}")
+            })
+            .collect::<Vec<_>>()
+            .join("\n\n");
+        let sources = self.format_sources(&ids);
+        Ok((embeddings, sources, ids))
+    }
+
+    fn resolve_source(&self, id: &DocumentId) -> String {
+        let (file_index, _) = id.split();
+        self.data
+            .files
+            .get(&file_index)
+            .map(|f| f.path.clone())
+            .unwrap_or_else(|| "unknown".to_string())
+    }
+
+    fn format_sources(&self, ids: &[DocumentId]) -> String {
+        let mut seen = IndexSet::new();
+        for id in ids {
+            let (file_index, _) = id.split();
+            if let Some(file) = self.data.files.get(&file_index) {
+                seen.insert(file.path.clone());
+            }
+        }
+        seen.into_iter()
+            .map(|path| format!("- {path}"))
+            .collect::<Vec<_>>()
+            .join("\n")
     }
 
     pub async fn sync_documents(