Fix find_project_root hijacking git worktrees nested under a Serena project (#1550)

* Fix find_project_root hijacking git worktrees nested under a Serena project

find_project_root searched all ancestor levels for .serena/project.yml
before ever looking for .git. A git worktree whose own .git is a pointer
file, nested under a directory that is an explicit Serena project, was
resolved to the ancestor project instead of the worktree. With CLI agents
that launch via --project-from-cwd (Claude Code, Codex, Gemini), this
silently bound the server to the wrong working tree: reads returned stale
symbols and edits landed in the parent repo.

Walk up in a single pass so the nearest project boundary wins, whether it
is a .serena/project.yml or a .git (dir or worktree/submodule pointer
file). Same-level behavior is unchanged. Adds a regression test.

* Document worktree project-root fix in changelog and usage docs

docs/02-usage/020_running.md

@@ -92,7 +92,9 @@ Some useful options include:
 
   * `--project <path|name>`: specify the project to work on by name or path.
   * `--project-from-cwd`: auto-detect the project from current working directory     
-    (looking for a directory containing `.serena/project.yml` or `.git` in parent directories and activating the containing directory as the project root, if any).
+    (walking up the parent directories and activating the nearest one that contains either `.serena/project.yml`
+    or `.git`, if any). The nearest boundary wins, so a git worktree nested under another Serena project resolves
+    to the worktree itself rather than the ancestor project.
     This option is intended for CLI-based agents like Claude Code, Gemini and Codex, which are typically started from within the project directory
     and which do not change directories during their operation.
   * `--language-backend JetBrains`: use the Serena JetBrains Plugin as the language backend (overriding the default backend configured in the central configuration)

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

@@ -14,3 +14,5 @@ having persisted the plan in a memory or dedicated file.
 [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).
 
 Be sure to add the `.serena` folder to version control, such that your project-specific settings and memories are available across worktrees.
+
+When you launch a CLI agent from inside a worktree using `--project-from-cwd`, Serena activates the worktree itself, even if the worktree lives under another Serena project (for example `<repo>/.claude/worktrees/<name>`, where Claude Code creates them natively). The nearest project boundary wins: the worktree's own `.git` pointer file takes precedence over an ancestor's `.serena/project.yml`, so file operations always resolve against the correct working tree.