Fix links in docs

docs/01-about/010_llm-integration.md

@@ -13,5 +13,5 @@ In general, Serena can be integrated with an LLM in several ways:
     * Extensions like Cline or Roo Code
     * Local clients like [OpenWebUI](https://docs.openwebui.com/openapi-servers/mcp), [Jan](https://jan.ai/docs/mcp-examples/browser/browserbase#enable-mcp), [Agno](https://docs.agno.com/introduction/playground) and others
 * by using [mcpo to connect it to ChatGPT](../03-special-guides/serena_on_chatgpt.md) or other clients that don't support MCP but do support tool calling via OpenAPI.
-* by incorporating Serena's tools into an agent framework of your choice, as illustrated [here](docs/custom_agent.md).
+* by incorporating Serena's tools into an agent framework of your choice, as illustrated [here](../03-special-guides/custom_agent).
   Serena's tool implementation is decoupled from the framework-specific code and can thus easily be adapted to any agent framework.

docs/01-about/020_programming-languages.md

@@ -61,4 +61,4 @@ With Serena, we provide direct, out-of-the-box support for:
   (requires installation of ZLS - Zig Language Server)
 
 Support for further languages can easily be added by providing a shallow adapter for a new language server implementation,
-see Serena's [memory on that](.serena/memories/adding_new_language_support_guide.md).
+see Serena's [memory on that](https://github.com/oraios/serena/blob/main/.serena/memories/adding_new_language_support_guide.md).

docs/02-usage/020_running.md

@@ -41,9 +41,10 @@ Explore the CLI to see some of the customization options that serena provides (m
     uv run --directory /abs/path/to/serena serena
     ```
 
+(docker)=
 #### Using Docker (Experimental)
 
-⚠️ Docker support is currently experimental with several limitations. Please read the [Docker documentation](DOCKER.md) for important caveats before using it.
+⚠️ Docker support is currently experimental with several limitations. Please read the [Docker documentation](https://github.com/oraios/serena/blob/main/DOCKER.md) for important caveats before using it.
 
 You can run the Serena MCP server directly via docker as follows,
 assuming that the projects you want to work on are all located in `/path/to/your/projects`:
@@ -60,7 +61,7 @@ Replace `/path/to/your/projects` with the absolute path to your projects directo
 
 Alternatively, use docker compose with the `compose.yml` file provided in the repository.
 
-See the [Docker documentation](DOCKER.md) for detailed setup instructions, configuration options, and known limitations.
+See the [Docker documentation](https://github.com/oraios/serena/blob/main/DOCKER.md) for detailed setup instructions, configuration options, and known limitations.
 
 #### Using Nix
 

docs/02-usage/040_workflow.md

@@ -36,6 +36,7 @@ For instance, when using `uvx`, run
 
 After creation, you can adjust the project settings in the generated `.serena/project.yml` file.
 
+(indexing)=
 #### Indexing
 
 Especially for larger project, it is advisable to index the project after creation (in order to avoid

docs/02-usage/050_configuration.md

@@ -17,7 +17,7 @@ Serena is configured in four places:
 
    (or use the `--directory` command version).
 2. In the arguments passed to the `start-mcp-server` in your client's config (see below),
-   which will apply to all sessions started by the respective client. In particular, the [context](#contexts) parameter
+   which will apply to all sessions started by the respective client. In particular, the [context](contexts) parameter
    should be set appropriately for Serena to be best adjusted to existing tools and capabilities of your client.
    See for a detailed explanation. You can override all entries from the `serena_config.yml` through command line arguments.
 3. In the `.serena/project.yml` file within your project. This will hold project-level configuration that is used whenever

docs/02-usage/070_security.md

@@ -9,4 +9,4 @@ Therefore, to reduce the risk of unintended consequences when using Serena, it i
   * monitor tool executions carefully (e.g. via your MCP client, provided that it supports it),
   * consider enabling read-only mode for your project (set `read_only: True` in project.yml) if you only want to analyze code without modifying it,
   * restrict the set of allowed tools via the [configuration](050_configuration),
-  * use a sandboxed environment for running Serena (e.g. by [using Docker](020_running.md#using-docker-experimental)).
+  * use a sandboxed environment for running Serena (e.g. by [using Docker](docker)).

docs/02-usage/999_additional-usage.md

@@ -27,4 +27,6 @@ should not occur too often, unless the task is very large or complicated.
 
 [git-worktree](https://git-scm.com/docs/git-worktree) can be an excellent way to parallelize your work. More on this in [Anthropic: Run parallel Claude Code sessions with Git worktrees](https://docs.claude.com/en/docs/claude-code/common-workflows#run-parallel-claude-code-sessions-with-git-worktrees).
 
-When it comes to serena AND git-worktree AND larger projects (that take longer to index), the recommended way is to COPY your `$ORIG_PROJECT/.serena/cache` to `$GIT_WORKTREE/.serena/cache`. After you have performed pre-indexing of your project described in [Project Activation & Indexing](#project-activation--indexing) section. To avoid having to re-index per each git work tree that you create. 
+When it comes to serena AND git-worktree AND larger projects (that take longer to index), 
+the recommended way is to COPY your `$ORIG_PROJECT/.serena/cache` to `$GIT_WORKTREE/.serena/cache`. 
+Perform [pre-indexing of your project](indexing) to avoid having to re-index per each worktree you create.