Restructure docs, improve texts (particular for Running Serena)

docs/02-usage/040_workflow.md

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+## The Project Workflow
+
+### Project Activation & Indexing
+
+If you are mostly working with the same project, you can configure to always activate it at startup
+by passing `--project <path_or_name>` to the `start-mcp-server` command in your client's MCP config.
+This is especially useful for clients which configure MCP servers on a per-project basis, like Claude Code.
+
+Otherwise, the recommended way is to just ask the LLM to activate a project by providing it an absolute path to, or,
+in case the project was activated in the past, by its name. The default project name is the directory name.
+
+* "Activate the project /path/to/my_project"
+* "Activate the project my_project"
+
+All projects that have been activated will be automatically added to your `serena_config.yml`, and for each
+project, the file `.serena/project.yml` will be generated. You can adjust the latter, e.g., by changing the name
+(which you refer to during the activation) or other options. Make sure to not have two different projects with the
+same name.
+
+ℹ️ For larger projects, we recommend that you index your project to accelerate Serena's tools; otherwise the first
+tool application may be very slow.
+To do so, run this from the project directory (or pass the path to the project as an argument):
+
+```shell
+uvx --from git+https://github.com/oraios/serena serena project index
+```
+
+(or use the `--directory` command version).
+
+### Onboarding and Memories
+
+By default, Serena will perform an **onboarding process** when
+it is started for the first time for a project.
+The goal of the onboarding is for Serena to get familiar with the project
+and to store memories, which it can then draw upon in future interactions.
+If an LLM should fail to complete the onboarding and does not actually write the
+respective memories to disk, you may need to ask it to do so explicitly.
+
+The onboarding will usually read a lot of content from the project, thus filling
+up the context. It can therefore be advisable to switch to another conversation
+once the onboarding is complete.
+After the onboarding, we recommend that you have a quick look at the memories and,
+if necessary, edit them or add additional ones.
+
+**Memories** are files stored in `.serena/memories/` in the project directory,
+which the agent can choose to read in subsequent interactions.
+Feel free to read and adjust them as needed; you can also add new ones manually.
+Every file in the `.serena/memories/` directory is a memory file.
+Whenever Serena starts working on a project, the list of memories is
+provided, and the agent can decide to read them.
+We found that memories can significantly improve the user experience with Serena.