docs: deep quality pass — expand 10 thin pages, fix specific issues (#4134)

Developer guide stubs expanded to full documentation:
- trajectory-format.md: 56→233 lines (JSONL format, ShareGPT example,
  normalization rules, reasoning markup, replay code)
- session-storage.md: 66→388 lines (SQLite schema, migration table,
  FTS5 search syntax, lineage queries, Python API examples)
- context-compression-and-caching.md: 72→321 lines (dual compression
  system, config defaults, 4-phase algorithm, before/after example,
  prompt caching mechanics, cache-aware patterns)
- tools-runtime.md: 65→246 lines (registry API, dispatch flow,
  availability checking, error wrapping, approval flow)
- prompt-assembly.md: 89→246 lines (concrete assembled prompt example,
  SOUL.md injection, context file discovery table)

User-facing pages expanded:
- docker.md: 62→224 lines (volumes, env forwarding, docker-compose,
  resource limits, troubleshooting)
- updating.md: 79→167 lines (update behavior, version checking,
  rollback instructions, Nix users)
- skins.md: 80→206 lines (all color/spinner/branding keys, built-in
  skin descriptions, full custom skin YAML template)

Hub pages improved:
- integrations/index.md: 25→82 lines (web search backends table,
  TTS/browser providers, quick config example)
- features/overview.md: added Integrations section with 6 missing links

Specific fixes:
- configuration.md: removed duplicate Gateway Streaming section
- mcp.md: removed internal "PR work" language
- plugins.md: added inline minimal plugin example (self-contained)

13 files changed, ~1700 lines added. Docusaurus build verified clean.
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@ -41,6 +41,163 @@ The cached system prompt is assembled in roughly this order:
When `skip_context_files` is set (e.g., subagent delegation), SOUL.md is not loaded and the hardcoded `DEFAULT_AGENT_IDENTITY` is used instead.
### Concrete example: assembled system prompt
Here is a simplified view of what the final system prompt looks like when all layers are present (comments show the source of each section):
```
# Layer 1: Agent Identity (from ~/.hermes/SOUL.md)
You are Hermes, an AI assistant created by Nous Research.
You are an expert software engineer and researcher.
You value correctness, clarity, and efficiency.
...
# Layer 2: Tool-aware behavior guidance
You have persistent memory across sessions. Save durable facts using
the memory tool: user preferences, environment details, tool quirks,
and stable conventions. Memory is injected into every turn, so keep
it compact and focused on facts that will still matter later.
...
When the user references something from a past conversation or you
suspect relevant cross-session context exists, use session_search
to recall it before asking them to repeat themselves.
# Tool-use enforcement (for GPT/Codex models only)
You MUST use your tools to take action — do not describe what you
would do or plan to do without actually doing it.
...
# Layer 3: Honcho static block (when active)
[Honcho personality/context data]
# Layer 4: Optional system message (from config or API)
[User-configured system message override]
# Layer 5: Frozen MEMORY snapshot
## Persistent Memory
- User prefers Python 3.12, uses pyproject.toml
- Default editor is nvim
- Working on project "atlas" in ~/code/atlas
- Timezone: US/Pacific
# Layer 6: Frozen USER profile snapshot
## User Profile
- Name: Alice
- GitHub: alice-dev
# Layer 7: Skills index
## Skills (mandatory)
Before replying, scan the skills below. If one clearly matches
your task, load it with skill_view(name) and follow its instructions.
...
<available_skills>
software-development:
- code-review: Structured code review workflow
- test-driven-development: TDD methodology
research:
- arxiv: Search and summarize arXiv papers
</available_skills>
# Layer 8: Context files (from project directory)
# Project Context
The following project context files have been loaded and should be followed:
## AGENTS.md
This is the atlas project. Use pytest for testing. The main
entry point is src/atlas/main.py. Always run `make lint` before
committing.
# Layer 9: Timestamp + session
Current time: 2026-03-30T14:30:00-07:00
Session: abc123
# Layer 10: Platform hint
You are a CLI AI Agent. Try not to use markdown but simple text
renderable inside a terminal.
```
## How SOUL.md appears in the prompt
`SOUL.md` lives at `~/.hermes/SOUL.md` and serves as the agent's identity — the very first section of the system prompt. The loading logic in `prompt_builder.py` works as follows:
```python
# From agent/prompt_builder.py (simplified)
def load_soul_md() -> Optional[str]:
soul_path = get_hermes_home() / "SOUL.md"
if not soul_path.exists():
return None
content = soul_path.read_text(encoding="utf-8").strip()
content = _scan_context_content(content, "SOUL.md") # Security scan
content = _truncate_content(content, "SOUL.md") # Cap at 20k chars
return content
```
When `load_soul_md()` returns content, it replaces the hardcoded `DEFAULT_AGENT_IDENTITY`. The `build_context_files_prompt()` function is then called with `skip_soul=True` to prevent SOUL.md from appearing twice (once as identity, once as a context file).
If `SOUL.md` doesn't exist, the system falls back to:
```
You are Hermes Agent, an intelligent AI assistant created by Nous Research.
You are helpful, knowledgeable, and direct. You assist users with a wide
range of tasks including answering questions, writing and editing code,
analyzing information, creative work, and executing actions via your tools.
You communicate clearly, admit uncertainty when appropriate, and prioritize
being genuinely useful over being verbose unless otherwise directed below.
Be targeted and efficient in your exploration and investigations.
```
## How context files are injected
`build_context_files_prompt()` uses a **priority system** — only one project context type is loaded (first match wins):
```python
# From agent/prompt_builder.py (simplified)
def build_context_files_prompt(cwd=None, skip_soul=False):
cwd_path = Path(cwd).resolve()
# Priority: first match wins — only ONE project context loaded
project_context = (
_load_hermes_md(cwd_path) # 1. .hermes.md / HERMES.md (walks to git root)
or _load_agents_md(cwd_path) # 2. AGENTS.md (cwd only)
or _load_claude_md(cwd_path) # 3. CLAUDE.md (cwd only)
or _load_cursorrules(cwd_path) # 4. .cursorrules / .cursor/rules/*.mdc
)
sections = []
if project_context:
sections.append(project_context)
# SOUL.md from HERMES_HOME (independent of project context)
if not skip_soul:
soul_content = load_soul_md()
if soul_content:
sections.append(soul_content)
if not sections:
return ""
return (
"# Project Context\n\n"
"The following project context files have been loaded "
"and should be followed:\n\n"
+ "\n".join(sections)
)
```
### Context file discovery details
| Priority | Files | Search scope | Notes |
|----------|-------|-------------|-------|
| 1 | `.hermes.md`, `HERMES.md` | CWD up to git root | Hermes-native project config |
| 2 | `AGENTS.md` | CWD only | Common agent instruction file |
| 3 | `CLAUDE.md` | CWD only | Claude Code compatibility |
| 4 | `.cursorrules`, `.cursor/rules/*.mdc` | CWD only | Cursor compatibility |
All context files are:
- **Security scanned** — checked for prompt injection patterns (invisible unicode, "ignore previous instructions", credential exfiltration attempts)
- **Truncated** — capped at 20,000 characters using 70/20 head/tail ratio with a truncation marker
- **YAML frontmatter stripped**`.hermes.md` frontmatter is removed (reserved for future config overrides)
## API-call-time-only layers
These are intentionally *not* persisted as part of the cached system prompt: