chore: fix .gitignore inline comments + add untracked code files

Inline # comments in gitignore are not supported — they were silently
breaking three patterns (data/checkpoints/, data/adapter-migration-state.json,
.claude/agents/.generated/). Moved comments to their own lines and added
missing entries for runtime dirs (data/audit/, data/logs/, etc.) and
temp files (.interaction_tmp.json, .design-build/, .taskmaster bak files).

Also tracks previously untracked legitimate files: scripts, tests, docs,
skills references, .env.example, taskmaster templates.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

.env.example

@@ -0,0 +1,12 @@
+# API Keys (Required to enable respective provider)
+ANTHROPIC_API_KEY="your_anthropic_api_key_here"       # Required: Format: sk-ant-api03-...
+PERPLEXITY_API_KEY="your_perplexity_api_key_here"     # Optional: Format: pplx-...
+OPENAI_API_KEY="your_openai_api_key_here"             # Optional, for OpenAI models. Format: sk-proj-...
+GOOGLE_API_KEY="your_google_api_key_here"             # Optional, for Google Gemini models.
+MISTRAL_API_KEY="your_mistral_key_here"               # Optional, for Mistral AI models.
+XAI_API_KEY="YOUR_XAI_KEY_HERE"                       # Optional, for xAI AI models.
+GROQ_API_KEY="YOUR_GROQ_KEY_HERE"                     # Optional, for Groq models.
+OPENROUTER_API_KEY="YOUR_OPENROUTER_KEY_HERE"         # Optional, for OpenRouter models.
+AZURE_OPENAI_API_KEY="your_azure_key_here"            # Optional, for Azure OpenAI models (requires endpoint in .taskmaster/config.json).
+OLLAMA_API_KEY="your_ollama_api_key_here"             # Optional: For remote Ollama servers that require authentication.
+GITHUB_API_KEY="your_github_api_key_here"             # Optional: For GitHub import/export features. Format: ghp_... or github_pat_...