Merge pull request 'feat: brain_update supersede verb + brain_get / brain_write read-after-write handle (#45)' (#46) from feat/brain-update-supersede into main

.aider.conventions.md

@@ -27,6 +27,14 @@ and climate/sustainability tech.
 
 These rules apply to every task across every project, regardless of harness.
 
+0. **Pre-task ritual — before ANY implementation (non-negotiable).** Run this before writing a single line:
+   - **Query the brain** (`brain_query`) for the domain + symptom. If the result changes your approach, surface it before acting. 5 seconds beats 5 hours.
+   - **Load the relevant skill** — see trigger table in *Engineering Skills* below.
+   - **Write the failing test first.** Name the test before the function. If the target is untestable (e.g. `main()` wiring), extract the logic into a testable function first. No implementation without a red test.
+   - **State the observable success criterion** — what specific behavior, output, or passing test proves this is done?
+
+   **TDD is non-negotiable.** "Tests pass" is not proof of correctness — only proof the tests ran. Write tests that would catch the bug before writing code that fixes it.
+
 1. **No assumptions.** Don't hide confusion — surface it. Surface tradeoffs explicitly.
    Think before coding; if the problem is unclear, ask or state assumptions before acting.
 2. **Minimum viable code.** Solve with the smallest change that works. Nothing
@@ -49,6 +57,22 @@ These rules apply to every task across every project, regardless of harness.
    PR flow only when a human reviewer outside the project is required. Document
    the reason in PROJECT.md.
 
+6. **Close the loop — every substantive task ends with the same ritual.** Shipping
+   the code is not the end of the task; capturing it is. Run this unprompted:
+   - **Tag + bump SemVer** on the change (annotated tag; minor for a feature or
+     new/changed ADR, patch for a fix; docs in the same commit). Check the repo's
+     actual last tag — stated versions in docs drift stale.
+   - **Push** main and the tag (CI is the gate).
+   - **Persist generalizable learnings to the brain** (`brain_write`, wing/hall) —
+     the reusable patterns and the footguns that would bite anyone again, never
+     project status. See *Knowledge base — when to write* below.
+   - **File discovered-but-deferred work as tracker issues** on the project's own
+     repo — token-budget gaps, recorded ADR limitations, v2 follow-ups. Don't let
+     "out of scope, recorded" rot in a commit message; make it a ticket with a
+     source pointer.
+   - Surface the brain entries and issue numbers in the closing summary so the
+     trail is auditable.
+
 ## Default stack
 
 | Layer | Default | Fallback | Last resort |
@@ -78,6 +102,26 @@ Exploratory: Rust, Zig — I'll tell you when I want these.
 - **Security**: no secrets in code, govulncheck before adding deps, SOPS for encrypted config
 - **Dependencies**: prefer stdlib. testify, slog, templ, sqlc, google.golang.org/adk (agent projects only) are pre-approved; anything else needs justification in the commit message
 
+## Secret handling (every harness, every command)
+
+Tool output is persisted: terminal → `~/.claude/projects` transcripts →
+claudewatcher → brain/wiki → gitea history. A secret printed once is
+searchable forever, and clearing it means rotating the key. So:
+
+1. **Never print, echo, log, or transform a secret to inspect it.** No
+   `base64`/`xxd`/`cat` of a key, and never pipe a secret through a transform
+   to defeat `op run`'s output masking (it masks raw values; base64 hides them
+   from the mask — that exact trick leaked a key on 2026-06-11).
+2. **Secrets stay in the subprocess.** Reference them only as env vars consumed
+   *inside* `op run --env-file ~/.op-env -- <cmd>`. Never place a literal secret
+   in a command's argv (it lands in the tool call and the transcript).
+3. **Existence check without revealing the value:** `[ -n "$X" ] && echo set` —
+   never `${X:-...}` (returns the value when set) and never echo a substring of it.
+4. **Cross-host secrets:** run the secret-consuming command on the host that has
+   the secret; do not forward a raw key over ssh argv/stdout.
+5. If a secret does leak into output, say so immediately and flag it for rotation —
+   don't bury it.
+
 ## Infrastructure
 
 Three machines on Tailscale:
@@ -157,7 +201,7 @@ entries that age well are about *why*, *how to avoid*, and *what to do when*.
 | **Claude Code, Claude Desktop** | `brain_query` (BM25), `brain_answer` (LLM-synth + sources) MCP tools | `brain_write` MCP tool |
 | **Crush, Pi, Antigravity, other MCP-capable** | same MCP server: `ingestion-brain` (via the `mcp__*_brain__*` namespace once authenticated) | same |
 | **Anything HTTP-only (curl, scripts)** | `POST https://brain-mcp.d-ma.be/query` with `{"query":"..."}` (auth via `BRAIN_MCP_TOKEN`) | `POST .../write` with `{"content":"...","filename":"..."}` |
-| **Browser / human inspection** | `https://gitea.d-ma.be/mathias/hyperguild` → `knowledge/` and `wiki/` markdown files |
+| **Browser / human inspection** | `https://git.d-ma.be/mathias/hyperguild` → `knowledge/` and `wiki/` markdown files |
 
 - **Scoping**: defaults to `public` collection; client projects filter to `{client}` + `public`.
 - **Routing**: brain_answer's LLM uses berget.ai as primary, iguana ollama as
@@ -219,15 +263,17 @@ unconditionally on every host, every harness.
 
 ## Engineering Skills
 
-Shared engineering skills are available in `~/dev/.skills/`. Load on demand via the index.
+Shared engineering skills are available in `~/dev/.skills/`. Load at task start — not "on demand" but on schedule, before writing code. See `~/dev/.skills/SKILLS_INDEX.md` for the full list.
 
-See `~/dev/.skills/SKILLS_INDEX.md` for the full list with descriptions and "use when" triggers.
+**Skill trigger table — load before starting, not after getting stuck:**
 
-Key skills:
-- **TDD**: always write tests first — load `tdd` skill
-- **Code Review**: load `code-review` skill before any review
-- **SOLID/Clean Code**: load `solid` or `clean-code` skill for design work
-- **Problem first**: load `problem-analysis` skill before coding non-trivial features
+| Task type | Load |
+|-----------|------|
+| Any feature or bug fix | `tdd` |
+| Refactor or design | `clean-code` or `solid` |
+| Debug | `problem-analysis` |
+| Review code or PRs | `code-review` |
+| Frame a problem before coding | `problem-analysis` |
 
 ---
 

.context/system-prompt.txt

@@ -32,6 +32,14 @@ and climate/sustainability tech.
 
 These rules apply to every task across every project, regardless of harness.
 
+0. **Pre-task ritual — before ANY implementation (non-negotiable).** Run this before writing a single line:
+   - **Query the brain** (`brain_query`) for the domain + symptom. If the result changes your approach, surface it before acting. 5 seconds beats 5 hours.
+   - **Load the relevant skill** — see trigger table in *Engineering Skills* below.
+   - **Write the failing test first.** Name the test before the function. If the target is untestable (e.g. `main()` wiring), extract the logic into a testable function first. No implementation without a red test.
+   - **State the observable success criterion** — what specific behavior, output, or passing test proves this is done?
+
+   **TDD is non-negotiable.** "Tests pass" is not proof of correctness — only proof the tests ran. Write tests that would catch the bug before writing code that fixes it.
+
 1. **No assumptions.** Don't hide confusion — surface it. Surface tradeoffs explicitly.
    Think before coding; if the problem is unclear, ask or state assumptions before acting.
 2. **Minimum viable code.** Solve with the smallest change that works. Nothing
@@ -54,6 +62,22 @@ These rules apply to every task across every project, regardless of harness.
    PR flow only when a human reviewer outside the project is required. Document
    the reason in PROJECT.md.
 
+6. **Close the loop — every substantive task ends with the same ritual.** Shipping
+   the code is not the end of the task; capturing it is. Run this unprompted:
+   - **Tag + bump SemVer** on the change (annotated tag; minor for a feature or
+     new/changed ADR, patch for a fix; docs in the same commit). Check the repo's
+     actual last tag — stated versions in docs drift stale.
+   - **Push** main and the tag (CI is the gate).
+   - **Persist generalizable learnings to the brain** (`brain_write`, wing/hall) —
+     the reusable patterns and the footguns that would bite anyone again, never
+     project status. See *Knowledge base — when to write* below.
+   - **File discovered-but-deferred work as tracker issues** on the project's own
+     repo — token-budget gaps, recorded ADR limitations, v2 follow-ups. Don't let
+     "out of scope, recorded" rot in a commit message; make it a ticket with a
+     source pointer.
+   - Surface the brain entries and issue numbers in the closing summary so the
+     trail is auditable.
+
 ## Default stack
 
 | Layer | Default | Fallback | Last resort |
@@ -83,6 +107,26 @@ Exploratory: Rust, Zig — I'll tell you when I want these.
 - **Security**: no secrets in code, govulncheck before adding deps, SOPS for encrypted config
 - **Dependencies**: prefer stdlib. testify, slog, templ, sqlc, google.golang.org/adk (agent projects only) are pre-approved; anything else needs justification in the commit message
 
+## Secret handling (every harness, every command)
+
+Tool output is persisted: terminal → `~/.claude/projects` transcripts →
+claudewatcher → brain/wiki → gitea history. A secret printed once is
+searchable forever, and clearing it means rotating the key. So:
+
+1. **Never print, echo, log, or transform a secret to inspect it.** No
+   `base64`/`xxd`/`cat` of a key, and never pipe a secret through a transform
+   to defeat `op run`'s output masking (it masks raw values; base64 hides them
+   from the mask — that exact trick leaked a key on 2026-06-11).
+2. **Secrets stay in the subprocess.** Reference them only as env vars consumed
+   *inside* `op run --env-file ~/.op-env -- <cmd>`. Never place a literal secret
+   in a command's argv (it lands in the tool call and the transcript).
+3. **Existence check without revealing the value:** `[ -n "$X" ] && echo set` —
+   never `${X:-...}` (returns the value when set) and never echo a substring of it.
+4. **Cross-host secrets:** run the secret-consuming command on the host that has
+   the secret; do not forward a raw key over ssh argv/stdout.
+5. If a secret does leak into output, say so immediately and flag it for rotation —
+   don't bury it.
+
 ## Infrastructure
 
 Three machines on Tailscale:
@@ -162,7 +206,7 @@ entries that age well are about *why*, *how to avoid*, and *what to do when*.
 | **Claude Code, Claude Desktop** | `brain_query` (BM25), `brain_answer` (LLM-synth + sources) MCP tools | `brain_write` MCP tool |
 | **Crush, Pi, Antigravity, other MCP-capable** | same MCP server: `ingestion-brain` (via the `mcp__*_brain__*` namespace once authenticated) | same |
 | **Anything HTTP-only (curl, scripts)** | `POST https://brain-mcp.d-ma.be/query` with `{"query":"..."}` (auth via `BRAIN_MCP_TOKEN`) | `POST .../write` with `{"content":"...","filename":"..."}` |
-| **Browser / human inspection** | `https://gitea.d-ma.be/mathias/hyperguild` → `knowledge/` and `wiki/` markdown files |
+| **Browser / human inspection** | `https://git.d-ma.be/mathias/hyperguild` → `knowledge/` and `wiki/` markdown files |
 
 - **Scoping**: defaults to `public` collection; client projects filter to `{client}` + `public`.
 - **Routing**: brain_answer's LLM uses berget.ai as primary, iguana ollama as
@@ -224,15 +268,17 @@ unconditionally on every host, every harness.
 
 ## Engineering Skills
 
-Shared engineering skills are available in `~/dev/.skills/`. Load on demand via the index.
+Shared engineering skills are available in `~/dev/.skills/`. Load at task start — not "on demand" but on schedule, before writing code. See `~/dev/.skills/SKILLS_INDEX.md` for the full list.
 
-See `~/dev/.skills/SKILLS_INDEX.md` for the full list with descriptions and "use when" triggers.
+**Skill trigger table — load before starting, not after getting stuck:**
 
-Key skills:
-- **TDD**: always write tests first — load `tdd` skill
-- **Code Review**: load `code-review` skill before any review
-- **SOLID/Clean Code**: load `solid` or `clean-code` skill for design work
-- **Problem first**: load `problem-analysis` skill before coding non-trivial features
+| Task type | Load |
+|-----------|------|
+| Any feature or bug fix | `tdd` |
+| Refactor or design | `clean-code` or `solid` |
+| Debug | `problem-analysis` |
+| Review code or PRs | `code-review` |
+| Frame a problem before coding | `problem-analysis` |
 
 ---
 

.cursorrules

@@ -30,6 +30,14 @@ and climate/sustainability tech.
 
 These rules apply to every task across every project, regardless of harness.
 
+0. **Pre-task ritual — before ANY implementation (non-negotiable).** Run this before writing a single line:
+   - **Query the brain** (`brain_query`) for the domain + symptom. If the result changes your approach, surface it before acting. 5 seconds beats 5 hours.
+   - **Load the relevant skill** — see trigger table in *Engineering Skills* below.
+   - **Write the failing test first.** Name the test before the function. If the target is untestable (e.g. `main()` wiring), extract the logic into a testable function first. No implementation without a red test.
+   - **State the observable success criterion** — what specific behavior, output, or passing test proves this is done?
+
+   **TDD is non-negotiable.** "Tests pass" is not proof of correctness — only proof the tests ran. Write tests that would catch the bug before writing code that fixes it.
+
 1. **No assumptions.** Don't hide confusion — surface it. Surface tradeoffs explicitly.
    Think before coding; if the problem is unclear, ask or state assumptions before acting.
 2. **Minimum viable code.** Solve with the smallest change that works. Nothing
@@ -52,6 +60,22 @@ These rules apply to every task across every project, regardless of harness.
    PR flow only when a human reviewer outside the project is required. Document
    the reason in PROJECT.md.
 
+6. **Close the loop — every substantive task ends with the same ritual.** Shipping
+   the code is not the end of the task; capturing it is. Run this unprompted:
+   - **Tag + bump SemVer** on the change (annotated tag; minor for a feature or
+     new/changed ADR, patch for a fix; docs in the same commit). Check the repo's
+     actual last tag — stated versions in docs drift stale.
+   - **Push** main and the tag (CI is the gate).
+   - **Persist generalizable learnings to the brain** (`brain_write`, wing/hall) —
+     the reusable patterns and the footguns that would bite anyone again, never
+     project status. See *Knowledge base — when to write* below.
+   - **File discovered-but-deferred work as tracker issues** on the project's own
+     repo — token-budget gaps, recorded ADR limitations, v2 follow-ups. Don't let
+     "out of scope, recorded" rot in a commit message; make it a ticket with a
+     source pointer.
+   - Surface the brain entries and issue numbers in the closing summary so the
+     trail is auditable.
+
 ## Default stack
 
 | Layer | Default | Fallback | Last resort |
@@ -81,6 +105,26 @@ Exploratory: Rust, Zig — I'll tell you when I want these.
 - **Security**: no secrets in code, govulncheck before adding deps, SOPS for encrypted config
 - **Dependencies**: prefer stdlib. testify, slog, templ, sqlc, google.golang.org/adk (agent projects only) are pre-approved; anything else needs justification in the commit message
 
+## Secret handling (every harness, every command)
+
+Tool output is persisted: terminal → `~/.claude/projects` transcripts →
+claudewatcher → brain/wiki → gitea history. A secret printed once is
+searchable forever, and clearing it means rotating the key. So:
+
+1. **Never print, echo, log, or transform a secret to inspect it.** No
+   `base64`/`xxd`/`cat` of a key, and never pipe a secret through a transform
+   to defeat `op run`'s output masking (it masks raw values; base64 hides them
+   from the mask — that exact trick leaked a key on 2026-06-11).
+2. **Secrets stay in the subprocess.** Reference them only as env vars consumed
+   *inside* `op run --env-file ~/.op-env -- <cmd>`. Never place a literal secret
+   in a command's argv (it lands in the tool call and the transcript).
+3. **Existence check without revealing the value:** `[ -n "$X" ] && echo set` —
+   never `${X:-...}` (returns the value when set) and never echo a substring of it.
+4. **Cross-host secrets:** run the secret-consuming command on the host that has
+   the secret; do not forward a raw key over ssh argv/stdout.
+5. If a secret does leak into output, say so immediately and flag it for rotation —
+   don't bury it.
+
 ## Infrastructure
 
 Three machines on Tailscale:
@@ -160,7 +204,7 @@ entries that age well are about *why*, *how to avoid*, and *what to do when*.
 | **Claude Code, Claude Desktop** | `brain_query` (BM25), `brain_answer` (LLM-synth + sources) MCP tools | `brain_write` MCP tool |
 | **Crush, Pi, Antigravity, other MCP-capable** | same MCP server: `ingestion-brain` (via the `mcp__*_brain__*` namespace once authenticated) | same |
 | **Anything HTTP-only (curl, scripts)** | `POST https://brain-mcp.d-ma.be/query` with `{"query":"..."}` (auth via `BRAIN_MCP_TOKEN`) | `POST .../write` with `{"content":"...","filename":"..."}` |
-| **Browser / human inspection** | `https://gitea.d-ma.be/mathias/hyperguild` → `knowledge/` and `wiki/` markdown files |
+| **Browser / human inspection** | `https://git.d-ma.be/mathias/hyperguild` → `knowledge/` and `wiki/` markdown files |
 
 - **Scoping**: defaults to `public` collection; client projects filter to `{client}` + `public`.
 - **Routing**: brain_answer's LLM uses berget.ai as primary, iguana ollama as
@@ -222,15 +266,17 @@ unconditionally on every host, every harness.
 
 ## Engineering Skills
 
-Shared engineering skills are available in `~/dev/.skills/`. Load on demand via the index.
+Shared engineering skills are available in `~/dev/.skills/`. Load at task start — not "on demand" but on schedule, before writing code. See `~/dev/.skills/SKILLS_INDEX.md` for the full list.
 
-See `~/dev/.skills/SKILLS_INDEX.md` for the full list with descriptions and "use when" triggers.
+**Skill trigger table — load before starting, not after getting stuck:**
 
-Key skills:
-- **TDD**: always write tests first — load `tdd` skill
-- **Code Review**: load `code-review` skill before any review
-- **SOLID/Clean Code**: load `solid` or `clean-code` skill for design work
-- **Problem first**: load `problem-analysis` skill before coding non-trivial features
+| Task type | Load |
+|-----------|------|
+| Any feature or bug fix | `tdd` |
+| Refactor or design | `clean-code` or `solid` |
+| Debug | `problem-analysis` |
+| Review code or PRs | `code-review` |
+| Frame a problem before coding | `problem-analysis` |
 
 ---
 

AGENTS.md

@@ -27,6 +27,14 @@ and climate/sustainability tech.
 
 These rules apply to every task across every project, regardless of harness.
 
+0. **Pre-task ritual — before ANY implementation (non-negotiable).** Run this before writing a single line:
+   - **Query the brain** (`brain_query`) for the domain + symptom. If the result changes your approach, surface it before acting. 5 seconds beats 5 hours.
+   - **Load the relevant skill** — see trigger table in *Engineering Skills* below.
+   - **Write the failing test first.** Name the test before the function. If the target is untestable (e.g. `main()` wiring), extract the logic into a testable function first. No implementation without a red test.
+   - **State the observable success criterion** — what specific behavior, output, or passing test proves this is done?
+
+   **TDD is non-negotiable.** "Tests pass" is not proof of correctness — only proof the tests ran. Write tests that would catch the bug before writing code that fixes it.
+
 1. **No assumptions.** Don't hide confusion — surface it. Surface tradeoffs explicitly.
    Think before coding; if the problem is unclear, ask or state assumptions before acting.
 2. **Minimum viable code.** Solve with the smallest change that works. Nothing
@@ -49,6 +57,22 @@ These rules apply to every task across every project, regardless of harness.
    PR flow only when a human reviewer outside the project is required. Document
    the reason in PROJECT.md.
 
+6. **Close the loop — every substantive task ends with the same ritual.** Shipping
+   the code is not the end of the task; capturing it is. Run this unprompted:
+   - **Tag + bump SemVer** on the change (annotated tag; minor for a feature or
+     new/changed ADR, patch for a fix; docs in the same commit). Check the repo's
+     actual last tag — stated versions in docs drift stale.
+   - **Push** main and the tag (CI is the gate).
+   - **Persist generalizable learnings to the brain** (`brain_write`, wing/hall) —
+     the reusable patterns and the footguns that would bite anyone again, never
+     project status. See *Knowledge base — when to write* below.
+   - **File discovered-but-deferred work as tracker issues** on the project's own
+     repo — token-budget gaps, recorded ADR limitations, v2 follow-ups. Don't let
+     "out of scope, recorded" rot in a commit message; make it a ticket with a
+     source pointer.
+   - Surface the brain entries and issue numbers in the closing summary so the
+     trail is auditable.
+
 ## Default stack
 
 | Layer | Default | Fallback | Last resort |
@@ -78,6 +102,26 @@ Exploratory: Rust, Zig — I'll tell you when I want these.
 - **Security**: no secrets in code, govulncheck before adding deps, SOPS for encrypted config
 - **Dependencies**: prefer stdlib. testify, slog, templ, sqlc, google.golang.org/adk (agent projects only) are pre-approved; anything else needs justification in the commit message
 
+## Secret handling (every harness, every command)
+
+Tool output is persisted: terminal → `~/.claude/projects` transcripts →
+claudewatcher → brain/wiki → gitea history. A secret printed once is
+searchable forever, and clearing it means rotating the key. So:
+
+1. **Never print, echo, log, or transform a secret to inspect it.** No
+   `base64`/`xxd`/`cat` of a key, and never pipe a secret through a transform
+   to defeat `op run`'s output masking (it masks raw values; base64 hides them
+   from the mask — that exact trick leaked a key on 2026-06-11).
+2. **Secrets stay in the subprocess.** Reference them only as env vars consumed
+   *inside* `op run --env-file ~/.op-env -- <cmd>`. Never place a literal secret
+   in a command's argv (it lands in the tool call and the transcript).
+3. **Existence check without revealing the value:** `[ -n "$X" ] && echo set` —
+   never `${X:-...}` (returns the value when set) and never echo a substring of it.
+4. **Cross-host secrets:** run the secret-consuming command on the host that has
+   the secret; do not forward a raw key over ssh argv/stdout.
+5. If a secret does leak into output, say so immediately and flag it for rotation —
+   don't bury it.
+
 ## Infrastructure
 
 Three machines on Tailscale:
@@ -157,7 +201,7 @@ entries that age well are about *why*, *how to avoid*, and *what to do when*.
 | **Claude Code, Claude Desktop** | `brain_query` (BM25), `brain_answer` (LLM-synth + sources) MCP tools | `brain_write` MCP tool |
 | **Crush, Pi, Antigravity, other MCP-capable** | same MCP server: `ingestion-brain` (via the `mcp__*_brain__*` namespace once authenticated) | same |
 | **Anything HTTP-only (curl, scripts)** | `POST https://brain-mcp.d-ma.be/query` with `{"query":"..."}` (auth via `BRAIN_MCP_TOKEN`) | `POST .../write` with `{"content":"...","filename":"..."}` |
-| **Browser / human inspection** | `https://gitea.d-ma.be/mathias/hyperguild` → `knowledge/` and `wiki/` markdown files |
+| **Browser / human inspection** | `https://git.d-ma.be/mathias/hyperguild` → `knowledge/` and `wiki/` markdown files |
 
 - **Scoping**: defaults to `public` collection; client projects filter to `{client}` + `public`.
 - **Routing**: brain_answer's LLM uses berget.ai as primary, iguana ollama as
@@ -219,15 +263,17 @@ unconditionally on every host, every harness.
 
 ## Engineering Skills
 
-Shared engineering skills are available in `~/dev/.skills/`. Load on demand via the index.
+Shared engineering skills are available in `~/dev/.skills/`. Load at task start — not "on demand" but on schedule, before writing code. See `~/dev/.skills/SKILLS_INDEX.md` for the full list.
 
-See `~/dev/.skills/SKILLS_INDEX.md` for the full list with descriptions and "use when" triggers.
+**Skill trigger table — load before starting, not after getting stuck:**
 
-Key skills:
-- **TDD**: always write tests first — load `tdd` skill
-- **Code Review**: load `code-review` skill before any review
-- **SOLID/Clean Code**: load `solid` or `clean-code` skill for design work
-- **Problem first**: load `problem-analysis` skill before coding non-trivial features
+| Task type | Load |
+|-----------|------|
+| Any feature or bug fix | `tdd` |
+| Refactor or design | `clean-code` or `solid` |
+| Debug | `problem-analysis` |
+| Review code or PRs | `code-review` |
+| Frame a problem before coding | `problem-analysis` |
 
 ---
 

ingestion/internal/api/frontmatter.go

@@ -0,0 +1,97 @@
+package api
+
+import "strings"
+
+// frontmatter is an ordered, line-preserving view of a note's YAML
+// frontmatter block. It deliberately avoids a full YAML round-trip: the
+// brain writes flat `key: value` frontmatter by hand, and a yaml.v3
+// re-marshal would reorder keys and strip comments. Preserving the
+// original lines verbatim keeps brain_update a surgical edit — only the
+// keys it manages (updated_at, supersedes, supersede_reason) change.
+type frontmatter struct {
+	lines []fmLine
+}
+
+// fmLine is one frontmatter line. For `key: value` lines, key and value
+// are populated; for blank lines, comments, or anything that isn't a
+// simple scalar pair, key is empty and raw holds the line verbatim.
+type fmLine struct {
+	key   string
+	value string
+	raw   string
+}
+
+// parseFrontmatter splits src into its frontmatter block and body. A
+// frontmatter block is recognised only when the file opens with a `---`
+// fence and a closing `---` fence follows. Otherwise the whole input is
+// the body and the returned frontmatter is empty.
+func parseFrontmatter(src string) (frontmatter, string) {
+	var fm frontmatter
+	if !strings.HasPrefix(src, "---\n") {
+		return fm, src
+	}
+	rest := src[len("---\n"):]
+	end := strings.Index(rest, "\n---\n")
+	if end < 0 {
+		// Opening fence with no closing fence — treat as bodyless content.
+		return fm, src
+	}
+	block := rest[:end]
+	body := rest[end+len("\n---\n"):]
+
+	for _, line := range strings.Split(block, "\n") {
+		key, val, ok := strings.Cut(line, ":")
+		key = strings.TrimSpace(key)
+		if !ok || key == "" || strings.HasPrefix(strings.TrimSpace(line), "#") {
+			fm.lines = append(fm.lines, fmLine{raw: line})
+			continue
+		}
+		fm.lines = append(fm.lines, fmLine{key: key, value: strings.TrimSpace(val)})
+	}
+	return fm, body
+}
+
+// get returns the value for key, or "" if absent.
+func (f *frontmatter) get(key string) string {
+	for _, l := range f.lines {
+		if l.key == key {
+			return l.value
+		}
+	}
+	return ""
+}
+
+// set overrides the value for an existing key in place, or appends a new
+// `key: value` line when the key is absent.
+func (f *frontmatter) set(key, value string) {
+	for i := range f.lines {
+		if f.lines[i].key == key {
+			f.lines[i].value = value
+			return
+		}
+	}
+	f.lines = append(f.lines, fmLine{key: key, value: value})
+}
+
+// render serialises the frontmatter back into a `---`-fenced block. An
+// empty frontmatter renders to the empty string so bodies without a
+// header stay header-less.
+func (f *frontmatter) render() string {
+	if len(f.lines) == 0 {
+		return ""
+	}
+	var b strings.Builder
+	b.WriteString("---\n")
+	for _, l := range f.lines {
+		if l.key == "" {
+			b.WriteString(l.raw)
+		} else {
+			b.WriteString(l.key)
+			b.WriteString(": ")
+			b.WriteString(l.value)
+		}
+		b.WriteByte('\n')
+	}
+	b.WriteString("---\n")
+	return b.String()
+}

ingestion/internal/api/frontmatter_test.go

@@ -0,0 +1,61 @@
+package api
+
+import (
+	"strings"
+	"testing"
+
+	"github.com/stretchr/testify/assert"
+)
+
+func TestParseFrontmatterSplitsHeaderAndBody(t *testing.T) {
+	src := "---\nwing: jepa-fx\nhall: facts\ncreated_at: 2026-01-01T00:00:00Z\n---\n# Title\n\nbody text\n"
+	fm, body := parseFrontmatter(src)
+
+	assert.Equal(t, "jepa-fx", fm.get("wing"))
+	assert.Equal(t, "facts", fm.get("hall"))
+	assert.Equal(t, "2026-01-01T00:00:00Z", fm.get("created_at"))
+	assert.Equal(t, "# Title\n\nbody text\n", body)
+}
+
+func TestParseFrontmatterNoHeader(t *testing.T) {
+	src := "# Just a body\n\nno frontmatter here\n"
+	fm, body := parseFrontmatter(src)
+
+	assert.Empty(t, fm.lines)
+	assert.Equal(t, src, body)
+}
+
+func TestFrontmatterSetOverridesExistingKey(t *testing.T) {
+	fm, _ := parseFrontmatter("---\nwing: a\nupdated_at: old\n---\nbody\n")
+	fm.set("updated_at", "new")
+
+	assert.Equal(t, "new", fm.get("updated_at"))
+	// No duplicate key.
+	assert.Equal(t, 1, strings.Count(fm.render(), "updated_at:"))
+}
+
+func TestFrontmatterSetAppendsNewKey(t *testing.T) {
+	fm, _ := parseFrontmatter("---\nwing: a\n---\nbody\n")
+	fm.set("supersedes", "abc123")
+
+	out := fm.render()
+	assert.Contains(t, out, "wing: a")
+	assert.Contains(t, out, "supersedes: abc123")
+}
+
+func TestFrontmatterRenderPreservesCustomFields(t *testing.T) {
+	src := "---\nwing: a\nhall: facts\ncustom_field: keep-me\ntags: [x, y]\n---\nbody\n"
+	fm, _ := parseFrontmatter(src)
+	fm.set("updated_at", "2026-06-22T00:00:00Z")
+
+	out := fm.render()
+	assert.Contains(t, out, "custom_field: keep-me")
+	assert.Contains(t, out, "tags: [x, y]")
+	assert.Contains(t, out, "updated_at: 2026-06-22T00:00:00Z")
+}
+
+func TestFrontmatterRenderRoundTrips(t *testing.T) {
+	src := "---\nwing: a\nhall: facts\n---\n"
+	fm, _ := parseFrontmatter(src)
+	assert.Equal(t, src, fm.render())
+}

ingestion/internal/api/update.go

@@ -0,0 +1,131 @@
+package api
+
+import (
+	"crypto/sha256"
+	"encoding/hex"
+	"fmt"
+	"os"
+	"path/filepath"
+	"strings"
+	"time"
+
+	"github.com/mathiasbq/hyperguild/ingestion/internal/brain"
+)
+
+// ContentHash returns the lowercase hex sha256 of b. It is the note's
+// content_hash handle: brain_write / brain_update return it, brain_get
+// recomputes it from the file on disk, and brain_update stamps the prior
+// note's hash into the new note's `supersedes` frontmatter.
+func ContentHash(b []byte) string {
+	sum := sha256.Sum256(b)
+	return hex.EncodeToString(sum[:])
+}
+
+// resolveWithin maps a brainDir-relative path to an absolute path and
+// guarantees it does not escape brainDir. Returns the cleaned relPath
+// (forward-slashed) and the absolute path.
+func resolveWithin(brainDir, relPath string) (rel, abs string, err error) {
+	clean := filepath.Clean("/" + filepath.ToSlash(relPath))
+	rel = strings.TrimPrefix(clean, "/")
+	abs = filepath.Join(brainDir, filepath.FromSlash(rel))
+	check, err := filepath.Rel(brainDir, abs)
+	if err != nil || check == ".." || strings.HasPrefix(check, ".."+string(filepath.Separator)) {
+		return "", "", fmt.Errorf("path %q escapes brain dir", relPath)
+	}
+	return rel, abs, nil
+}
+
+// UpdateNoteOptions identifies the note to supersede and supplies its new
+// body. Path takes precedence; otherwise the target is resolved from
+// Wing/Hall/Slug via brain.NotePath.
+type UpdateNoteOptions struct {
+	Path    string // brainDir-relative path; takes precedence over wing/hall/slug
+	Wing    string
+	Hall    string
+	Slug    string
+	Content string // new full body (whole-note replace)
+	Reason  string // optional; stamped as supersede_reason
+}
+
+// UpdateNote supersedes an existing note in place. It replaces the body
+// with opts.Content, preserves the existing frontmatter (created_at,
+// wing, hall, and any custom fields), and stamps updated_at, supersedes
+// (the prior content hash), and supersede_reason (when given).
+//
+// It never creates: if the target does not exist, it returns an error so
+// the caller can fall back to brain_write. Returns the note's relPath,
+// the new content hash, and the prior content hash.
+//
+// Embeddings are NOT refreshed here. The rewritten file's mtime advances,
+// which the mtime-driven vectorstore.Sync ticker uses to re-embed it on
+// its next pass — the same out-of-band mechanism brain_write relies on.
+func UpdateNote(brainDir string, opts UpdateNoteOptions) (relPath, contentHash, priorHash string, err error) {
+	if opts.Content == "" {
+		return "", "", "", fmt.Errorf("content is required")
+	}
+
+	var rel string
+	if opts.Path != "" {
+		rel = opts.Path
+	} else {
+		full, perr := brain.NotePath(brainDir, opts.Wing, opts.Hall, opts.Slug)
+		if perr != nil {
+			return "", "", "", perr
+		}
+		rel, _ = filepath.Rel(brainDir, full)
+		rel = filepath.ToSlash(rel)
+	}
+
+	rel, abs, err := resolveWithin(brainDir, rel)
+	if err != nil {
+		return "", "", "", err
+	}
+
+	prior, err := os.ReadFile(abs)
+	if err != nil {
+		if os.IsNotExist(err) {
+			return "", "", "", fmt.Errorf("note %q does not exist: use brain_write to create", rel)
+		}
+		return "", "", "", fmt.Errorf("read target: %w", err)
+	}
+	priorHash = ContentHash(prior)
+
+	fm, _ := parseFrontmatter(string(prior))
+	fm.set("updated_at", time.Now().UTC().Format(time.RFC3339))
+	fm.set("supersedes", priorHash)
+	if opts.Reason != "" {
+		fm.set("supersede_reason", opts.Reason)
+	}
+
+	out := []byte(fm.render() + opts.Content)
+	if err := os.WriteFile(abs, out, 0o644); err != nil {
+		return "", "", "", fmt.Errorf("write: %w", err)
+	}
+	return rel, ContentHash(out), priorHash, nil
+}
+
+// ReadNote reads the note at the brainDir-relative relPath and returns
+// its parsed frontmatter, body, and content hash. It is the read-after-
+// write primitive behind brain_get: the hash it returns equals the hash
+// brain_write / brain_update returned for the same bytes.
+func ReadNote(brainDir, relPath string) (fm map[string]string, body, contentHash string, err error) {
+	_, abs, err := resolveWithin(brainDir, relPath)
+	if err != nil {
+		return nil, "", "", err
+	}
+	raw, err := os.ReadFile(abs)
+	if err != nil {
+		if os.IsNotExist(err) {
+			return nil, "", "", fmt.Errorf("note %q does not exist", relPath)
+		}
+		return nil, "", "", fmt.Errorf("read note: %w", err)
+	}
+	parsed, body := parseFrontmatter(string(raw))
+	fm = make(map[string]string, len(parsed.lines))
+	for _, l := range parsed.lines {
+		if l.key != "" {
+			fm[l.key] = l.value
+		}
+	}
+	return fm, body, ContentHash(raw), nil
+}

ingestion/internal/api/update_test.go

@@ -0,0 +1,130 @@
+package api
+
+import (
+	"os"
+	"path/filepath"
+	"strings"
+	"testing"
+
+	"github.com/stretchr/testify/assert"
+	"github.com/stretchr/testify/require"
+)
+
+// seedNote writes a note directly to disk and returns its relPath.
+func seedNote(t *testing.T, brainDir, rel, content string) string {
+	t.Helper()
+	full := filepath.Join(brainDir, filepath.FromSlash(rel))
+	require.NoError(t, os.MkdirAll(filepath.Dir(full), 0o755))
+	require.NoError(t, os.WriteFile(full, []byte(content), 0o644))
+	return rel
+}
+
+func TestUpdateNoteSupersedesAndStamps(t *testing.T) {
+	brainDir := t.TempDir()
+	rel := seedNote(t, brainDir, "wiki/jepa-fx/facts/val-vol.md",
+		"---\nwing: jepa-fx\nhall: facts\ncreated_at: 2026-01-01T00:00:00Z\ncustom: keep-me\n---\n# Old\n\nold body\n")
+
+	relPath, hash, priorHash, err := UpdateNote(brainDir, UpdateNoteOptions{
+		Path:    rel,
+		Content: "# New\n\nnew body\n",
+		Reason:  "facts changed",
+	})
+	require.NoError(t, err)
+	assert.Equal(t, rel, relPath)
+	assert.NotEmpty(t, hash)
+	assert.NotEmpty(t, priorHash)
+	assert.NotEqual(t, hash, priorHash)
+
+	got, err := os.ReadFile(filepath.Join(brainDir, filepath.FromSlash(rel)))
+	require.NoError(t, err)
+	s := string(got)
+	// Body replaced.
+	assert.Contains(t, s, "# New")
+	assert.NotContains(t, s, "old body")
+	// Prior fields preserved.
+	assert.Contains(t, s, "wing: jepa-fx")
+	assert.Contains(t, s, "hall: facts")
+	assert.Contains(t, s, "created_at: 2026-01-01T00:00:00Z")
+	assert.Contains(t, s, "custom: keep-me")
+	// Supersession stamped.
+	assert.Contains(t, s, "updated_at:")
+	assert.Contains(t, s, "supersedes: "+priorHash)
+	assert.Contains(t, s, "supersede_reason: facts changed")
+}
+
+func TestUpdateNoteResolvesByWingHallSlug(t *testing.T) {
+	brainDir := t.TempDir()
+	seedNote(t, brainDir, "wiki/jepa-fx/facts/val-vol.md",
+		"---\nwing: jepa-fx\nhall: facts\n---\nold\n")
+
+	relPath, _, _, err := UpdateNote(brainDir, UpdateNoteOptions{
+		Wing: "jepa-fx", Hall: "facts", Slug: "val-vol",
+		Content: "new\n",
+	})
+	require.NoError(t, err)
+	assert.Equal(t, "wiki/jepa-fx/facts/val-vol.md", relPath)
+}
+
+func TestUpdateNoteErrorsOnMissingAndDoesNotCreate(t *testing.T) {
+	brainDir := t.TempDir()
+
+	_, _, _, err := UpdateNote(brainDir, UpdateNoteOptions{
+		Wing: "jepa-fx", Hall: "facts", Slug: "ghost",
+		Content: "x\n",
+	})
+	require.Error(t, err)
+	assert.Contains(t, err.Error(), "does not exist")
+
+	// No file created.
+	_, statErr := os.Stat(filepath.Join(brainDir, "wiki/jepa-fx/facts/ghost.md"))
+	assert.True(t, os.IsNotExist(statErr), "missing-target update must not create a note")
+}
+
+func TestUpdateNoteRejectsTraversal(t *testing.T) {
+	brainDir := t.TempDir()
+	_, _, _, err := UpdateNote(brainDir, UpdateNoteOptions{
+		Path:    "../escape.md",
+		Content: "x\n",
+	})
+	require.Error(t, err)
+}
+
+func TestReadNoteReturnsFrontmatterBodyHash(t *testing.T) {
+	brainDir := t.TempDir()
+	rel := seedNote(t, brainDir, "wiki/jepa-fx/facts/n.md",
+		"---\nwing: jepa-fx\nhall: facts\n---\n# Body\n\ntext\n")
+
+	fm, body, hash, err := ReadNote(brainDir, rel)
+	require.NoError(t, err)
+	assert.Equal(t, "jepa-fx", fm["wing"])
+	assert.Equal(t, "facts", fm["hall"])
+	assert.Equal(t, "# Body\n\ntext\n", body)
+
+	// Hash matches ContentHash of the raw bytes on disk (round-trip).
+	raw, _ := os.ReadFile(filepath.Join(brainDir, filepath.FromSlash(rel)))
+	assert.Equal(t, ContentHash(raw), hash)
+}
+
+func TestReadNoteRejectsTraversal(t *testing.T) {
+	brainDir := t.TempDir()
+	_, _, _, err := ReadNote(brainDir, "../../etc/passwd")
+	require.Error(t, err)
+}
+
+func TestUpdateThenReadRoundTripsHash(t *testing.T) {
+	brainDir := t.TempDir()
+	rel := seedNote(t, brainDir, "wiki/a/facts/n.md", "---\nwing: a\nhall: facts\n---\nold\n")
+
+	_, hash, _, err := UpdateNote(brainDir, UpdateNoteOptions{Path: rel, Content: "new\n"})
+	require.NoError(t, err)
+
+	_, _, readHash, err := ReadNote(brainDir, rel)
+	require.NoError(t, err)
+	assert.Equal(t, hash, readHash, "update content_hash must round-trip through ReadNote")
+}
+
+func TestContentHashStable(t *testing.T) {
+	assert.Equal(t, ContentHash([]byte("abc")), ContentHash([]byte("abc")))
+	assert.NotEqual(t, ContentHash([]byte("abc")), ContentHash([]byte("abd")))
+	assert.True(t, strings.HasPrefix(ContentHash([]byte("")), "")) // hex, non-panicking
+}

ingestion/internal/mcp/brain_update_test.go

@@ -0,0 +1,204 @@
+package mcp_test
+
+import (
+	"context"
+	"encoding/json"
+	"os"
+	"path/filepath"
+	"strings"
+	"testing"
+	"time"
+
+	"github.com/mathiasbq/hyperguild/ingestion/internal/mcp"
+	"github.com/mathiasbq/hyperguild/ingestion/internal/vectorstore"
+	"github.com/stretchr/testify/assert"
+	"github.com/stretchr/testify/require"
+)
+
+// callResult parses the JSON text payload of a successful tool call.
+func callResult(t *testing.T, resp map[string]any) map[string]any {
+	t.Helper()
+	require.Nil(t, resp["error"], "tool returned error: %v", resp["error"])
+	text := resp["result"].(map[string]any)["content"].([]any)[0].(map[string]any)["text"].(string)
+	var out map[string]any
+	require.NoError(t, json.Unmarshal([]byte(text), &out))
+	return out
+}
+
+func TestBrainUpdateSupersedesExisting(t *testing.T) {
+	brainDir := t.TempDir()
+	srv := mcp.NewServer(brainDir, nil, nil, nil)
+
+	// Seed via brain_write so the note carries real frontmatter.
+	callResult(t, toolCall(t, srv, "brain_write", map[string]any{
+		"content": "# Old\n\nold body\n", "filename": "val-vol",
+		"wing": "jepa-fx", "hall": "facts",
+	}))
+
+	out := callResult(t, toolCall(t, srv, "brain_update", map[string]any{
+		"wing": "jepa-fx", "hall": "facts", "slug": "val-vol",
+		"content": "# New\n\nnew body\n", "reason": "facts changed",
+	}))
+	assert.Equal(t, "wiki/jepa-fx/facts/val-vol.md", out["path"])
+	assert.Equal(t, out["path"], out["id"])
+	assert.NotEmpty(t, out["content_hash"])
+	assert.Equal(t, true, out["superseded"])
+
+	got, err := os.ReadFile(filepath.Join(brainDir, "wiki/jepa-fx/facts/val-vol.md"))
+	require.NoError(t, err)
+	s := string(got)
+	assert.Contains(t, s, "# New")
+	assert.NotContains(t, s, "old body")
+	assert.Contains(t, s, "wing: jepa-fx")
+	assert.Contains(t, s, "supersede_reason: facts changed")
+	assert.Contains(t, s, "supersedes:")
+}
+
+func TestBrainUpdateMissingTargetErrorsNoCreate(t *testing.T) {
+	brainDir := t.TempDir()
+	srv := mcp.NewServer(brainDir, nil, nil, nil)
+
+	resp := toolCall(t, srv, "brain_update", map[string]any{
+		"wing": "jepa-fx", "hall": "facts", "slug": "ghost",
+		"content": "x\n",
+	})
+	require.NotNil(t, resp["error"])
+	assert.Contains(t, resp["error"].(map[string]any)["message"].(string), "does not exist")
+	_, statErr := os.Stat(filepath.Join(brainDir, "wiki/jepa-fx/facts/ghost.md"))
+	assert.True(t, os.IsNotExist(statErr))
+}
+
+func TestBrainUpdateByFullPath(t *testing.T) {
+	brainDir := t.TempDir()
+	srv := mcp.NewServer(brainDir, nil, nil, nil)
+	callResult(t, toolCall(t, srv, "brain_write", map[string]any{
+		"content": "old\n", "filename": "n", "wing": "a", "hall": "facts",
+	}))
+
+	out := callResult(t, toolCall(t, srv, "brain_update", map[string]any{
+		"slug": "wiki/a/facts/n.md", "content": "fresh\n",
+	}))
+	assert.Equal(t, "wiki/a/facts/n.md", out["path"])
+}
+
+func TestBrainGetByIDAndPath(t *testing.T) {
+	brainDir := t.TempDir()
+	srv := mcp.NewServer(brainDir, nil, nil, nil)
+	w := callResult(t, toolCall(t, srv, "brain_write", map[string]any{
+		"content": "# Body\n\ntext\n", "filename": "n", "wing": "a", "hall": "facts",
+	}))
+	id := w["id"].(string)
+	hash := w["content_hash"].(string)
+	require.NotEmpty(t, id)
+	require.NotEmpty(t, hash)
+
+	// by id
+	g1 := callResult(t, toolCall(t, srv, "brain_get", map[string]any{"id": id}))
+	assert.Equal(t, id, g1["path"])
+	assert.Equal(t, hash, g1["content_hash"], "content_hash must round-trip write→get")
+	assert.Contains(t, g1["body"].(string), "# Body")
+	fm := g1["frontmatter"].(map[string]any)
+	assert.Equal(t, "a", fm["wing"])
+
+	// by path
+	g2 := callResult(t, toolCall(t, srv, "brain_get", map[string]any{"path": id}))
+	assert.Equal(t, hash, g2["content_hash"])
+}
+
+func TestBrainGetMissingArgsErrors(t *testing.T) {
+	srv := mcp.NewServer(t.TempDir(), nil, nil, nil)
+	resp := toolCall(t, srv, "brain_get", map[string]any{})
+	require.NotNil(t, resp["error"])
+}
+
+func TestBrainWriteReturnsHandle(t *testing.T) {
+	brainDir := t.TempDir()
+	srv := mcp.NewServer(brainDir, nil, nil, nil)
+	out := callResult(t, toolCall(t, srv, "brain_write", map[string]any{
+		"content": "# X\n\nbody\n", "filename": "x", "wing": "a", "hall": "facts",
+	}))
+	assert.Equal(t, "wiki/a/facts/x.md", out["path"])
+	assert.Equal(t, out["path"], out["id"])
+	assert.NotEmpty(t, out["content_hash"])
+}
+
+// --- retrieval-reflects-new-content: exercises the real mtime-driven Sync ---
+
+type fakeVecStore struct {
+	chunks  map[string][]float32
+	deleted []string
+}
+
+func (f *fakeVecStore) KnownPathsWithTime(_ context.Context) (map[string]time.Time, error) {
+	m := make(map[string]time.Time, len(f.chunks))
+	for p := range f.chunks {
+		m[p] = time.Unix(0, 0) // always stale → mtime(now) is always newer
+	}
+	return m, nil
+}
+
+func (f *fakeVecStore) Upsert(_ context.Context, path string, vec []float32) error {
+	f.chunks[path] = vec
+	return nil
+}
+
+func (f *fakeVecStore) Delete(_ context.Context, path string) error {
+	delete(f.chunks, path)
+	f.deleted = append(f.deleted, path)
+	return nil
+}
+
+type fakeEmbedder struct{ seen []string }
+
+func (e *fakeEmbedder) Embed(_ context.Context, text string) ([]float32, error) {
+	e.seen = append(e.seen, text)
+	return []float32{1, 0, 0}, nil
+}
+
+// TestBrainUpdateReembedsNewContent proves the supersede contract end to
+// end against the actual embedding mechanism: brain_update rewrites the
+// file, advancing its mtime, and the next vectorstore.Sync pass re-embeds
+// the NEW body and drops the stale chunk. No stub of the re-index path.
+func TestBrainUpdateReembedsNewContent(t *testing.T) {
+	brainDir := t.TempDir()
+	srv := mcp.NewServer(brainDir, nil, nil, nil)
+	ctx := context.Background()
+
+	callResult(t, toolCall(t, srv, "brain_write", map[string]any{
+		"content": "# Note\n\nthe OLD distinctive payload\n",
+		"filename": "n", "wing": "a", "hall": "facts",
+	}))
+
+	store := &fakeVecStore{chunks: map[string][]float32{}}
+	emb := &fakeEmbedder{}
+
+	// First sync embeds the original content.
+	_, err := vectorstore.Sync(ctx, brainDir, store, emb)
+	require.NoError(t, err)
+	require.NotEmpty(t, store.chunks)
+	require.True(t, anyContains(emb.seen, "OLD distinctive payload"))
+
+	callResult(t, toolCall(t, srv, "brain_update", map[string]any{
+		"wing": "a", "hall": "facts", "slug": "n",
+		"content": "# Note\n\nthe NEW distinctive payload\n",
+	}))
+
+	emb.seen = nil // only watch what the second pass embeds
+	_, err = vectorstore.Sync(ctx, brainDir, store, emb)
+	require.NoError(t, err)
+
+	assert.True(t, anyContains(emb.seen, "NEW distinctive payload"),
+		"Sync must re-embed the superseded body; saw %v", emb.seen)
+	assert.False(t, anyContains(emb.seen, "OLD distinctive payload"),
+		"the old body must not be re-embedded")
+	assert.NotEmpty(t, store.deleted, "stale chunks must be deleted before re-embed")
+}
+
+func anyContains(ss []string, sub string) bool {
+	for _, s := range ss {
+		if strings.Contains(s, sub) {
+			return true
+		}
+	}
+	return false
+}

ingestion/internal/mcp/handlers.go

@@ -61,6 +61,26 @@ func (s *Server) tools() []map[string]any {
 				"hall":     enum("optional memory type (requires wing)", halls...),
 			}),
 		},
+		{
+			"name":        "brain_update",
+			"description": "Supersede an existing brain note in place: whole-note body replace + frontmatter re-stamp (updated_at, supersedes=prior content hash, supersede_reason). Errors if the target does not exist — use brain_write to create. Returns {id, path, content_hash, superseded}. Prior version recoverable from git.",
+			"inputSchema": schema([]string{"content"}, map[string]any{
+				"content": str("new full body (whole-note replace)"),
+				"slug":    str("target note slug within wing/hall, OR a full brain-relative path (e.g. wiki/jepa-fx/facts/x.md)"),
+				"wing":    str("wing of the target (required unless slug/path is a full path)"),
+				"hall":    enum("hall of the target (required unless slug/path is a full path)", halls...),
+				"path":    str("full brain-relative path to the target; takes precedence over slug/wing/hall"),
+				"reason":  str("optional short note on why superseded — stamped into frontmatter"),
+			}),
+		},
+		{
+			"name":        "brain_get",
+			"description": "Fetch a single brain note by id or path (both are the brain-relative path — the note handle). Returns {id, path, content_hash, frontmatter, body}. Read-after-write confirmation without a lexical re-query.",
+			"inputSchema": schema([]string{}, map[string]any{
+				"id":   str("note id (brain-relative path) as returned by brain_write/brain_update"),
+				"path": str("brain-relative path to the note; equivalent to id"),
+			}),
+		},
 		{
 			"name":        "brain_tunnel",
 			"description": "Create an explicit bidirectional [[wikilink]] between two notes in different wings. Idempotent.",
@@ -222,7 +242,111 @@ func (s *Server) brainWrite(ctx context.Context, args json.RawMessage) (json.Raw
 		}
 	}
 	s.indexInGraph(ctx, "brain_write", relPath)
-	return json.Marshal(map[string]string{"path": relPath})
+	// Read-after-write handle: id == relPath, content_hash == sha256 of
+	// the bytes just written. path is kept for backward compatibility.
+	_, _, hash, _ := api.ReadNote(s.brainDir, relPath)
+	return json.Marshal(map[string]string{"id": relPath, "path": relPath, "content_hash": hash})
+}
+
+type brainUpdateArgs struct {
+	Slug    string `json:"slug,omitempty"`
+	Wing    string `json:"wing,omitempty"`
+	Hall    string `json:"hall,omitempty"`
+	Path    string `json:"path,omitempty"`
+	Content string `json:"content"`
+	Reason  string `json:"reason,omitempty"`
+}
+
+// brainUpdate supersedes an existing note in place: whole-note body
+// replace, frontmatter re-stamp (updated_at/supersedes/supersede_reason),
+// graph re-index, and wing _index rebuild. It never creates — a missing
+// target is an error so the caller can fall back to brain_write.
+//
+// Embedding re-sync is delegated to the out-of-band vectorstore.Sync
+// ticker: the rewritten file's mtime advances, so the next pass re-embeds
+// it. This mirrors brain_write, which likewise does not embed in-handler.
+func (s *Server) brainUpdate(ctx context.Context, args json.RawMessage) (json.RawMessage, error) {
+	var a brainUpdateArgs
+	if err := json.Unmarshal(args, &a); err != nil {
+		return nil, fmt.Errorf("parse args: %w", err)
+	}
+	if a.Content == "" {
+		return nil, fmt.Errorf("content is required")
+	}
+
+	opts := api.UpdateNoteOptions{Content: a.Content, Reason: a.Reason}
+	switch {
+	case a.Path != "":
+		opts.Path = a.Path
+	case strings.Contains(a.Slug, "/"):
+		// slug carries a full path (issue #45: "slug ... OR full path").
+		opts.Path = a.Slug
+	default:
+		opts.Wing, opts.Hall, opts.Slug = a.Wing, a.Hall, a.Slug
+	}
+
+	relPath, hash, _, err := api.UpdateNote(s.brainDir, opts)
+	if err != nil {
+		return nil, err
+	}
+
+	// Best-effort wiki upkeep, mirroring brain_write: rebuild the wing
+	// _index and re-tunnel cross-wing matches against the new body. Both
+	// are idempotent and never block — the note is already superseded.
+	if wing := wingFromRelPath(relPath); wing != "" {
+		if err := brain.BuildWingIndex(s.brainDir, wing); err != nil {
+			slog.Warn("brain_update: auto-index failed", "wing", wing, "err", err)
+		}
+		if err := brain.AutoTunnel(s.brainDir, relPath, a.Content); err != nil {
+			slog.Warn("brain_update: auto-tunnel failed", "src", relPath, "err", err)
+		}
+	}
+	s.indexInGraph(ctx, "brain_update", relPath)
+
+	return json.Marshal(map[string]any{
+		"id": relPath, "path": relPath, "content_hash": hash, "superseded": true,
+	})
+}
+
+// wingFromRelPath extracts the wing segment from a structured wiki path
+// (wiki/<wing>/<hall>/<slug>.md). Returns "" for legacy/non-wiki paths.
+func wingFromRelPath(relPath string) string {
+	parts := strings.Split(relPath, "/")
+	if len(parts) >= 4 && parts[0] == "wiki" {
+		return parts[1]
+	}
+	return ""
+}
+
+type brainGetArgs struct {
+	ID   string `json:"id,omitempty"`
+	Path string `json:"path,omitempty"`
+}
+
+// brainGet fetches a note by id or path (both are the brainDir-relative
+// path — the de-facto handle). Read-only; the create-path read-after-
+// write primitive that lets callers confirm a write landed without a
+// lexical re-query.
+func (s *Server) brainGet(_ context.Context, args json.RawMessage) (json.RawMessage, error) {
+	var a brainGetArgs
+	if err := json.Unmarshal(args, &a); err != nil {
+		return nil, fmt.Errorf("parse args: %w", err)
+	}
+	target := a.Path
+	if target == "" {
+		target = a.ID
+	}
+	if target == "" {
+		return nil, fmt.Errorf("id or path is required")
+	}
+	fm, body, hash, err := api.ReadNote(s.brainDir, target)
+	if err != nil {
+		return nil, err
+	}
+	return json.Marshal(map[string]any{
+		"id": target, "path": target, "content_hash": hash,
+		"frontmatter": fm, "body": body,
+	})
 }
 
 // indexInGraph is a best-effort wrapper around graphsync.IndexDoc that

ingestion/internal/mcp/server.go

@@ -1,7 +1,7 @@
 // Package mcp implements an MCP HTTP handler for the ingestion service.
-// Exposed tools: brain_query, brain_write, brain_index, brain_tunnel,
-// brain_ingest, brain_ingest_raw, brain_answer, brain_classify,
-// brain_graph, brain_context, session_log.
+// Exposed tools: brain_query, brain_write, brain_update, brain_get,
+// brain_index, brain_tunnel, brain_ingest, brain_ingest_raw,
+// brain_answer, brain_classify, brain_graph, brain_context, session_log.
 package mcp
 
 import (
@@ -177,6 +177,10 @@ func (s *Server) handleCall(ctx context.Context, name string, args json.RawMessa
 		return s.brainQuery(ctx, args)
 	case "brain_write":
 		return s.brainWrite(ctx, args)
+	case "brain_update":
+		return s.brainUpdate(ctx, args)
+	case "brain_get":
+		return s.brainGet(ctx, args)
 	case "brain_index":
 		return s.brainIndex(ctx, args)
 	case "brain_tunnel":

ingestion/internal/mcp/server_test.go

@@ -55,7 +55,8 @@ func TestServerToolsList(t *testing.T) {
 		names = append(names, t.(map[string]any)["name"].(string))
 	}
 	assert.ElementsMatch(t, []string{
-		"brain_query", "brain_write", "brain_index", "brain_tunnel",
+		"brain_query", "brain_write", "brain_update", "brain_get",
+		"brain_index", "brain_tunnel",
 		"brain_ingest_raw", "brain_ingest",
 		"brain_answer", "brain_classify", "brain_graph", "brain_context",
 		"session_log",