Add ignore_all_dot_files config option; fix Pyright dot-directory indexing

[EarthmanWeb]

Problem

Serena unconditionally ignores all dot-prefixed directories (e.g.
.github, .config, .devcontainer) via is_ignored_dirname().
This is the right default for most cases, but breaks legitimate
workflows:

• .github/ workflows: teams that store YAML, scripts or
  documentation in .github/ cannot get symbol support for those files
• .config/ or .devcontainer/: project config files in
  dot-directories are invisible to Serena

Additionally, Pyright has its own internal dot-directory exclusion that
is separate from Serena's. Even when Serena's exclusion was adjusted,
Pyright would still skip dot-directories because its initializationOptions
excluded **/.venv etc., and its own defaults excluded **/.*.
Pyright also sends workspace/configuration requests to fetch
python.analysis settings — these were previously unhandled, causing
silent misconfiguration.

Fix

New config option: ignore_all_dot_files (default: true)

Added to ProjectConfig, LanguageServerConfig, and
project.template.yml. When set to false:

• SolidLanguageServer.is_ignored_dirname() only ignores .git
  unconditionally; all other dot-directories are traversed
• PyrightServer._get_initialize_params() becomes an instance method
  and builds exclude/include lists based on ignore_all_dot_files:
  • false: adds include: ["."] to override Pyright's internal
    dot-directory exclusion
  • true: keeps existing behaviour (excludes .venv, .env, .pixi)
• PyrightServer now handles workspace/configuration requests,
  returning appropriate python.analysis include/exclude settings

Example

# .serena/project.yml
ignore_all_dot_files: false  # enable symbol retrieval in .github/, etc.

# Before: .github/workflows/ci.yml invisible to Serena
get_symbols_overview(".github/workflows/ci.yml")
# → FileNotFoundError or empty (directory ignored)

# After:
get_symbols_overview(".github/workflows/ci.yml")
# → {"on": {}, "jobs": {...}}