doc: update Quick Start & Architecture in README (#2947)

* doc: TOC, Quick Start, Architecture

Overhaul README to improve developer onboarding and documentation. Adds a Table of Contents, Quick Start (TL;DR + detailed Docker, binary, and build-from-source instructions), verification steps, and a Module Map. Expands Features into bullet points and introduces detailed Architecture sections including ASCII and Mermaid diagrams, a deployment comparison table, and module overview. Adds contributor guidance, community/contact info, and ecosystem links. Also updates .serena/project.yml to set project_name and include placeholders for base/default modes, included optional tools, and fixed_tools to enable per-project Serena configuration.

Author: imbajin

.serena/project.yml

@@ -79,6 +79,27 @@ excluded_tools: []
 # initial prompt for the project. It will always be given to the LLM upon activating the project
 # (contrary to the memories, which are loaded on demand).
 initial_prompt: ""
-
+# the name by which the project can be referenced within Serena
 project_name: "server"
+
+# list of tools to include that would otherwise be disabled (particularly optional tools that are disabled by default)
 included_optional_tools: []
+
+# list of mode names to that are always to be included in the set of active modes
+# The full set of modes to be activated is base_modes + default_modes.
+# If the setting is undefined, the base_modes from the global configuration (serena_config.yml) apply.
+# Otherwise, this setting overrides the global configuration.
+# Set this to [] to disable base modes for this project.
+# Set this to a list of mode names to always include the respective modes for this project.
+base_modes:
+
+# list of mode names that are to be activated by default.
+# The full set of modes to be activated is base_modes + default_modes.
+# If the setting is undefined, the default_modes from the global configuration (serena_config.yml) apply.
+# Otherwise, this overrides the setting from the global configuration (serena_config.yml).
+# This setting can, in turn, be overridden by CLI parameters (--mode).
+default_modes:
+
+# fixed set of tools to use as the base tool set (if non-empty), replacing Serena's default set of tools.
+# This cannot be combined with non-empty excluded_tools or included_optional_tools.
+fixed_tools: []