chore: reorganize project structure and add new scripts

- Rename and relocate markdown files for better organization
- Update references in command files to reflect new paths
- Add new implementation and chore planning scripts
- Update .gitignore to include agentic runs output

Author: MarkusNeusinger

.claude/commands/bug.md

@@ -6,7 +6,8 @@
       "Bash",
       "WebFetch",
       "mcp__plugin_serena_serena__*",
-      "mcp__plugin_context7_context7__*"
+      "mcp__plugin_context7_context7__*",
+      "mcp__plugin_playwright_playwright__*"
     ],
     "ask": [
       "Bash(git commit *)",

.claude/commands/check.md

@@ -227,6 +227,9 @@ nul
 # Project-specific
 temp/
 
+# Agentic runs output
+agentic/runs/
+
 # Additional environment files
 .env.local
 .env.production

.claude/commands/chore.md

@@ -24,6 +24,9 @@
 languages:
 - python
 - typescript
+
+# the encoding used by text files in the project
+# For a list of possible encodings, see https://docs.python.org/3.11/library/codecs.html#standard-encodings
 encoding: "utf-8"
 
 # whether to use project's .gitignore files to ignore files
@@ -82,7 +85,27 @@ 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: "pyplots"
+
+# list of tools to include that would otherwise be disabled (particularly optional tools that are disabled by default)
 included_optional_tools: []
+
+# 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: []
+
+# 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: