@zigrivers/scaffold 3.32.0 → 3.33.0

package/content/guides/knowledge-freshness/index.html

@@ -1442,7 +1442,7 @@ yesterday's signals still aggregate tomorrow; suppression filters the <em>emit</
 step, not the aggregation step (<span class="fp" data-path="src/observability/checks/lens-i-knowledge-gaps.ts:155">src/observability/checks/lens-i-knowledge-gaps.ts:155</span>).
 Signals only fade as they age out of the 90-day window naturally.</p>
 <h2 id="system-map">System map</h2>
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default" id="my-svg-flowchart-RESOLVER-18" transform="translate(785.453125, 333.2999954223633)"><rect class="basic label-container" style="" x="-122.765625" y="-42.099998474121094" width="245.53125" height="84.19999694824219"></rect><g class="label" style="" transform="translate(0, -27.099998474121094)"><rect></rect><g><rect class="background" style="stroke: none"></rect><text y="-10.1" style=""><tspan class="text-outer-tspan row" x="0" y="-0.1em"><tspan class="text-inner-tspan">3-tier</tspan><tspan class="text-inner-tspan"> --knowledge-root</tspan></tspan><tspan class="text-outer-tspan row" x="0" y="1em"><tspan class="text-inner-tspan">resolver</tspan></tspan><tspan class="text-outer-tspan row" x="0" y="2.1em"><tspan class="text-inner-tspan">suppresses</tspan><tspan class="text-inner-tspan"> covered</tspan><tspan class="text-inner-tspan"> topics</tspan></tspan></text></g></g></g></g></g></g><defs></defs><defs></defs></svg></figure>
 <p>Three real hooks sit beside the two arms: the <strong>phase-audit hook</strong> (runs Lens H
 only, never Lens I), the <strong>doc-conformance MMR channel</strong> (routes Lens I findings
 into MMR), and the <strong><code>--fix</code> flow</strong> (initial + verifier + postfix audit). They
@@ -1993,7 +1993,7 @@ maintainers want this URL to be the verbatim grounding for a P0/P1 finding?"</p>
 <h3 id="most-cited-hosts">Most-cited hosts</h3>
 <p>Counted live from every entry's <code>sources[*].url</code> at build time.</p>
 
-<div class="chart-block"><div class="chart chart-bar"><div class="chart-row" aria-label="martinfowler.com: 37"><span class="chart-label">martinfowler.com</span><div class="chart-bar" style="width:100%"></div></div><div class="chart-row" aria-label="developer.mozilla.org: 24"><span class="chart-label">developer.mozilla.org</span><div class="chart-bar" style="width:65%"></div></div><div class="chart-row" aria-label="owasp.org: 17"><span class="chart-label">owasp.org</span><div class="chart-bar" style="width:46%"></div></div><div class="chart-row" aria-label="developer.android.com: 15"><span class="chart-label">developer.android.com</span><div class="chart-bar" style="width:41%"></div></div><div class="chart-row" aria-label="the-turing-way.netlify.app: 15"><span class="chart-label">the-turing-way.netlify.app</span><div class="chart-bar" style="width:41%"></div></div><div class="chart-row" aria-label="developer.apple.com: 14"><span class="chart-label">developer.apple.com</span><div class="chart-bar" style="width:38%"></div></div><div class="chart-row" aria-label="developer.chrome.com: 14"><span class="chart-label">developer.chrome.com</span><div class="chart-bar" style="width:38%"></div></div><div class="chart-row" aria-label="sre.google: 12"><span class="chart-label">sre.google</span><div class="chart-bar" style="width:32%"></div></div><div class="chart-row" aria-label="w3.org: 12"><span class="chart-label">w3.org</span><div class="chart-bar" style="width:32%"></div></div><div class="chart-row" aria-label="microservices.io: 11"><span class="chart-label">microservices.io</span><div class="chart-bar" style="width:30%"></div></div><div class="chart-row" aria-label="ethereum.org: 10"><span class="chart-label">ethereum.org</span><div class="chart-bar" style="width:27%"></div></div><div class="chart-row" aria-label="rfc-editor.org: 10"><span class="chart-label">rfc-editor.org</span><div class="chart-bar" style="width:27%"></div></div><div class="chart-row" aria-label="consensys.github.io: 9"><span class="chart-label">consensys.github.io</span><div class="chart-bar" style="width:24%"></div></div><div class="chart-row" aria-label="docs.openzeppelin.com: 9"><span class="chart-label">docs.openzeppelin.com</span><div class="chart-bar" style="width:24%"></div></div><div class="chart-row" aria-label="opentelemetry.io: 9"><span class="chart-label">opentelemetry.io</span><div class="chart-bar" style="width:24%"></div></div></div>
+<div class="chart-block"><div class="chart chart-bar"><div class="chart-row" aria-label="martinfowler.com: 37"><span class="chart-label">martinfowler.com</span><div class="chart-bar" style="width:100%"></div></div><div class="chart-row" aria-label="developer.mozilla.org: 24"><span class="chart-label">developer.mozilla.org</span><div class="chart-bar" style="width:65%"></div></div><div class="chart-row" aria-label="modelcontextprotocol.io: 19"><span class="chart-label">modelcontextprotocol.io</span><div class="chart-bar" style="width:51%"></div></div><div class="chart-row" aria-label="owasp.org: 17"><span class="chart-label">owasp.org</span><div class="chart-bar" style="width:46%"></div></div><div class="chart-row" aria-label="developer.android.com: 15"><span class="chart-label">developer.android.com</span><div class="chart-bar" style="width:41%"></div></div><div class="chart-row" aria-label="the-turing-way.netlify.app: 15"><span class="chart-label">the-turing-way.netlify.app</span><div class="chart-bar" style="width:41%"></div></div><div class="chart-row" aria-label="developer.apple.com: 14"><span class="chart-label">developer.apple.com</span><div class="chart-bar" style="width:38%"></div></div><div class="chart-row" aria-label="developer.chrome.com: 14"><span class="chart-label">developer.chrome.com</span><div class="chart-bar" style="width:38%"></div></div><div class="chart-row" aria-label="sre.google: 12"><span class="chart-label">sre.google</span><div class="chart-bar" style="width:32%"></div></div><div class="chart-row" aria-label="w3.org: 12"><span class="chart-label">w3.org</span><div class="chart-bar" style="width:32%"></div></div><div class="chart-row" aria-label="microservices.io: 11"><span class="chart-label">microservices.io</span><div class="chart-bar" style="width:30%"></div></div><div class="chart-row" aria-label="rfc-editor.org: 11"><span class="chart-label">rfc-editor.org</span><div class="chart-bar" style="width:30%"></div></div><div class="chart-row" aria-label="ethereum.org: 10"><span class="chart-label">ethereum.org</span><div class="chart-bar" style="width:27%"></div></div><div class="chart-row" aria-label="consensys.github.io: 9"><span class="chart-label">consensys.github.io</span><div class="chart-bar" style="width:24%"></div></div><div class="chart-row" aria-label="docs.openzeppelin.com: 9"><span class="chart-label">docs.openzeppelin.com</span><div class="chart-bar" style="width:24%"></div></div></div>
 
 
 
@@ -2062,7 +2062,7 @@ maintainers want this URL to be the verbatim grounding for a P0/P1 finding?"</p>
 
 
 
-<table><thead><tr><th>Host</th><th>Citations</th></tr></thead><tbody><tr><td>martinfowler.com</td><td>37</td></tr><tr><td>developer.mozilla.org</td><td>24</td></tr><tr><td>owasp.org</td><td>17</td></tr><tr><td>developer.android.com</td><td>15</td></tr><tr><td>the-turing-way.netlify.app</td><td>15</td></tr><tr><td>developer.apple.com</td><td>14</td></tr><tr><td>developer.chrome.com</td><td>14</td></tr><tr><td>sre.google</td><td>12</td></tr><tr><td>w3.org</td><td>12</td></tr><tr><td>microservices.io</td><td>11</td></tr><tr><td>ethereum.org</td><td>10</td></tr><tr><td>rfc-editor.org</td><td>10</td></tr><tr><td>consensys.github.io</td><td>9</td></tr><tr><td>docs.openzeppelin.com</td><td>9</td></tr><tr><td>opentelemetry.io</td><td>9</td></tr></tbody></table></div>
+<table><thead><tr><th>Host</th><th>Citations</th></tr></thead><tbody><tr><td>martinfowler.com</td><td>37</td></tr><tr><td>developer.mozilla.org</td><td>24</td></tr><tr><td>modelcontextprotocol.io</td><td>19</td></tr><tr><td>owasp.org</td><td>17</td></tr><tr><td>developer.android.com</td><td>15</td></tr><tr><td>the-turing-way.netlify.app</td><td>15</td></tr><tr><td>developer.apple.com</td><td>14</td></tr><tr><td>developer.chrome.com</td><td>14</td></tr><tr><td>sre.google</td><td>12</td></tr><tr><td>w3.org</td><td>12</td></tr><tr><td>microservices.io</td><td>11</td></tr><tr><td>rfc-editor.org</td><td>11</td></tr><tr><td>ethereum.org</td><td>10</td></tr><tr><td>consensys.github.io</td><td>9</td></tr><tr><td>docs.openzeppelin.com</td><td>9</td></tr></tbody></table></div>
 
 <h3 id="the-full-allowlist">The full allowlist</h3>
 <p>Every host plus its category, and the pinned GitHub repos.</p>
@@ -2271,7 +2271,7 @@ maintainers want this URL to be the verbatim grounding for a P0/P1 finding?"</p>
 <h3 id="kb-inventory">KB inventory</h3>
 <p>Totals over <code>content/knowledge/</code>, broken down per category.</p>
 
-<p><strong>266 entries</strong> across 19 categories:</p>
+<p><strong>278 entries</strong> across 20 categories:</p>
 
 
 
@@ -2357,7 +2357,11 @@ maintainers want this URL to be the verbatim grounding for a P0/P1 finding?"</p>
 
 
 
-<table><thead><tr><th>Category</th><th>Entries</th></tr></thead><tbody><tr><td>core</td><td>35</td></tr><tr><td>game</td><td>25</td></tr><tr><td>research</td><td>25</td></tr><tr><td>backend</td><td>22</td></tr><tr><td>review</td><td>20</td></tr><tr><td>web-app</td><td>17</td></tr><tr><td>web3</td><td>14</td></tr><tr><td>data-science</td><td>13</td></tr><tr><td>browser-extension</td><td>12</td></tr><tr><td>data-pipeline</td><td>12</td></tr><tr><td>library</td><td>12</td></tr><tr><td>ml</td><td>12</td></tr><tr><td>mobile-app</td><td>12</td></tr><tr><td>cli</td><td>10</td></tr><tr><td>validation</td><td>7</td></tr><tr><td>product</td><td>6</td></tr><tr><td>execution</td><td>5</td></tr><tr><td>tools</td><td>4</td></tr><tr><td>finalization</td><td>3</td></tr></tbody></table>
+
+
+
+
+<table><thead><tr><th>Category</th><th>Entries</th></tr></thead><tbody><tr><td>core</td><td>35</td></tr><tr><td>game</td><td>25</td></tr><tr><td>research</td><td>25</td></tr><tr><td>backend</td><td>22</td></tr><tr><td>review</td><td>20</td></tr><tr><td>web-app</td><td>17</td></tr><tr><td>web3</td><td>14</td></tr><tr><td>data-science</td><td>13</td></tr><tr><td>browser-extension</td><td>12</td></tr><tr><td>data-pipeline</td><td>12</td></tr><tr><td>library</td><td>12</td></tr><tr><td>mcp-server</td><td>12</td></tr><tr><td>ml</td><td>12</td></tr><tr><td>mobile-app</td><td>12</td></tr><tr><td>cli</td><td>10</td></tr><tr><td>validation</td><td>7</td></tr><tr><td>product</td><td>6</td></tr><tr><td>execution</td><td>5</td></tr><tr><td>tools</td><td>4</td></tr><tr><td>finalization</td><td>3</td></tr></tbody></table>
 
 <h3 id="how-to-expand-the-allowlist">How to expand the allowlist</h3>
 <p>Adding a host is a one-line PR to

package/content/guides/knowledge-freshness/index.md

@@ -75,7 +75,7 @@ grounded LLM"]
   end
   subgraph gap[Gap arm]
     TAIL["gap-signal-tail
-89 pipeline steps"] --> EVENT["scaffold observe event
+90 pipeline steps"] --> EVENT["scaffold observe event
 knowledge_gap_signal"]
     EVENT --> LEDGER["ledger
 activity.jsonl"]
@@ -519,6 +519,7 @@ Counted live from every entry's `sources[*].url` at build time.
 | --- | --- |
 | martinfowler.com | 37 |
 | developer.mozilla.org | 24 |
+| modelcontextprotocol.io | 19 |
 | owasp.org | 17 |
 | developer.android.com | 15 |
 | the-turing-way.netlify.app | 15 |
@@ -527,11 +528,10 @@ Counted live from every entry's `sources[*].url` at build time.
 | sre.google | 12 |
 | w3.org | 12 |
 | microservices.io | 11 |
+| rfc-editor.org | 11 |
 | ethereum.org | 10 |
-| rfc-editor.org | 10 |
 | consensys.github.io | 9 |
 | docs.openzeppelin.com | 9 |
-| opentelemetry.io | 9 |
 :::
 <!-- /gen:host-citations -->
 
@@ -602,7 +602,7 @@ Every host plus its category, and the pinned GitHub repos.
 Totals over `content/knowledge/`, broken down per category.
 
 <!-- gen:kb-inventory -->
-**266 entries** across 19 categories:
+**278 entries** across 20 categories:
 
 | Category | Entries |
 | --- | --- |
@@ -617,6 +617,7 @@ Totals over `content/knowledge/`, broken down per category.
 | browser-extension | 12 |
 | data-pipeline | 12 |
 | library | 12 |
+| mcp-server | 12 |
 | ml | 12 |
 | mobile-app | 12 |
 | cli | 10 |

package/content/guides/multi-agent/index.html

@@ -1380,11 +1380,11 @@ test run.</p>
 <p>A <strong>git worktree</strong> solves this: it is an independent working directory backed by
 the <em>same</em> <code>.git</code> repository. Each agent gets its own files and its own checked-out
 branch, but commits, refs and history are shared. The layout is one primary
-checkout plus one sibling directory per agent:</p>
-<pre><code class="language-text">~/projects/
-├── scaffold/                  # primary checkout (you work here)
-├── scaffold-alpha/            # worktree for agent "alpha"
-└── scaffold-beta/             # worktree for agent "beta"
+checkout with all agent worktrees project-local under <code>.worktrees/</code>:</p>
+<pre><code class="language-text">scaffold/                      # primary checkout (you work here)
+└── .worktrees/                # agent worktrees (gitignored)
+    ├── alpha/                 # worktree for agent "alpha"
+    └── beta/                  # worktree for agent "beta"
 </code></pre>
 <p>So worktrees give you <strong>filesystem isolation with a shared object store</strong>:
 agents never overwrite each other's working files, but a PR merged from one
@@ -1398,20 +1398,21 @@ branch.</p></div>
 one parallel agent. Given a name like <code>alpha</code>, it:</p>
 <ol>
 <li><strong>Normalizes the name</strong> to a lowercase, hyphenated, alphanumeric slug (so
-<code>Agent_1</code> becomes <code>agent-1</code>), then derives the worktree directory as a
-<em>sibling</em> of the primary repo: <code>../&#x3C;repo-name>-&#x3C;slug></code>.</li>
+<code>Agent_1</code> becomes <code>agent-1</code>), then derives the worktree directory project-local
+under the primary repo: <code>.worktrees/&#x3C;slug></code>. It also ensures <code>.worktrees/</code> is
+gitignored so the worktree's checkout is never accidentally committed.</li>
 <li><strong>Creates the workspace branch</strong> <code>&#x3C;slug>-workspace</code> if it does not already
-exist <span class="fp" data-path="scripts/setup-agent-worktree.sh:40">scripts/setup-agent-worktree.sh:40</span>, then adds the worktree on
-that branch <span class="fp" data-path="scripts/setup-agent-worktree.sh:44">scripts/setup-agent-worktree.sh:44</span>. Re-running for an
+exist <span class="fp" data-path="scripts/setup-agent-worktree.sh:62">scripts/setup-agent-worktree.sh:62</span>, then adds the worktree on
+that branch <span class="fp" data-path="scripts/setup-agent-worktree.sh:65">scripts/setup-agent-worktree.sh:65</span>. Re-running for an
 existing worktree is a safe no-op.</li>
 <li><strong>Writes <code>.scaffold/identity.json</code></strong> — the stable identity that build
 observability stamps onto every event this worktree records. The script
-creates <code>.scaffold/</code> <span class="fp" data-path="scripts/setup-agent-worktree.sh:52">scripts/setup-agent-worktree.sh:52</span> and, only if no
+creates <code>.scaffold/</code> <span class="fp" data-path="scripts/setup-agent-worktree.sh:73">scripts/setup-agent-worktree.sh:73</span> and, only if no
 identity file exists yet, writes <code>worktree_id</code> (a UUID), <code>worktree_label</code>
 (the agent slug), and <code>created_at</code>
-<span class="fp" data-path="scripts/setup-agent-worktree.sh:71">scripts/setup-agent-worktree.sh:71</span>.</li>
+<span class="fp" data-path="scripts/setup-agent-worktree.sh:92">scripts/setup-agent-worktree.sh:92</span>.</li>
 <li><strong>Re-syncs Beads</strong> with a fail-soft <code>bd doctor --fix</code> when a <code>.beads/</code>
-directory is present <span class="fp" data-path="scripts/setup-agent-worktree.sh:88">scripts/setup-agent-worktree.sh:88</span>, reconciling the
+directory is present <span class="fp" data-path="scripts/setup-agent-worktree.sh:109">scripts/setup-agent-worktree.sh:109</span>, reconciling the
 worktree's Beads git hooks and project config against the installed <code>bd</code>
 version. (Beads DB sharing is automatic — worktrees discover the main repo's
 task DB via git's common directory, so there is nothing for <code>bd doctor</code> to
@@ -1467,8 +1468,8 @@ into needless conflicts.</li>
 </ul>
 <p>Each agent otherwise follows the standard PR workflow from its own worktree:
 branch, commit, push, <code>gh pr create</code>, wait for CI, squash-merge. The shared
-object store means a merge from <code>scaffold-alpha</code> is on <code>main</code> for everyone the
-moment it lands.</p>
+object store means a merge from agent <code>alpha</code>'s worktree is on <code>main</code> for
+everyone the moment it lands.</p>
 <h2 id="teardown-harvest">Teardown &#x26; harvest</h2>
 <p>When an agent's work is merged, retire its worktree. The single command for this
 is <code>scripts/teardown-agent-worktree.sh &#x3C;worktree-path></code>, and the <strong>order of
@@ -1529,7 +1530,7 @@ worktree — the CLI rejects a worktree primary root
 morning — does <strong>not</strong> mean re-running setup. The worktree and its
 <code>identity.json</code> persist on disk. Instead:</p>
 <ol>
-<li>Return to the agent's worktree directory (<code>../&#x3C;repo>-&#x3C;agent></code>).</li>
+<li>Return to the agent's worktree directory (<code>.worktrees/&#x3C;agent></code>).</li>
 <li>Run <strong><code>multi-agent-resume &#x3C;agent-name></code></strong> (or <code>single-agent-resume</code> for the
 non-worktree case). It verifies the worktree environment, syncs with <code>main</code>,
 reconciles task status against any PRs merged while you were away, and

package/content/guides/multi-agent/index.md

@@ -18,13 +18,13 @@ test run.
 A **git worktree** solves this: it is an independent working directory backed by
 the *same* `.git` repository. Each agent gets its own files and its own checked-out
 branch, but commits, refs and history are shared. The layout is one primary
-checkout plus one sibling directory per agent:
+checkout with all agent worktrees project-local under `.worktrees/`:
 
 ```text
-~/projects/
-├── scaffold/                  # primary checkout (you work here)
-├── scaffold-alpha/            # worktree for agent "alpha"
-└── scaffold-beta/             # worktree for agent "beta"
+scaffold/                      # primary checkout (you work here)
+└── .worktrees/                # agent worktrees (gitignored)
+    ├── alpha/                 # worktree for agent "alpha"
+    └── beta/                  # worktree for agent "beta"
 ```
 
 So worktrees give you **filesystem isolation with a shared object store**:
@@ -44,20 +44,21 @@ branch.
 one parallel agent. Given a name like `alpha`, it:
 
 1. **Normalizes the name** to a lowercase, hyphenated, alphanumeric slug (so
-   `Agent_1` becomes `agent-1`), then derives the worktree directory as a
-   *sibling* of the primary repo: `../<repo-name>-<slug>`.
+   `Agent_1` becomes `agent-1`), then derives the worktree directory project-local
+   under the primary repo: `.worktrees/<slug>`. It also ensures `.worktrees/` is
+   gitignored so the worktree's checkout is never accidentally committed.
 2. **Creates the workspace branch** `<slug>-workspace` if it does not already
-   exist :cite[scripts/setup-agent-worktree.sh:40], then adds the worktree on
-   that branch :cite[scripts/setup-agent-worktree.sh:44]. Re-running for an
+   exist :cite[scripts/setup-agent-worktree.sh:62], then adds the worktree on
+   that branch :cite[scripts/setup-agent-worktree.sh:65]. Re-running for an
    existing worktree is a safe no-op.
 3. **Writes `.scaffold/identity.json`** — the stable identity that build
    observability stamps onto every event this worktree records. The script
-   creates `.scaffold/` :cite[scripts/setup-agent-worktree.sh:52] and, only if no
+   creates `.scaffold/` :cite[scripts/setup-agent-worktree.sh:73] and, only if no
    identity file exists yet, writes `worktree_id` (a UUID), `worktree_label`
    (the agent slug), and `created_at`
-   :cite[scripts/setup-agent-worktree.sh:71].
+   :cite[scripts/setup-agent-worktree.sh:92].
 4. **Re-syncs Beads** with a fail-soft `bd doctor --fix` when a `.beads/`
-   directory is present :cite[scripts/setup-agent-worktree.sh:88], reconciling the
+   directory is present :cite[scripts/setup-agent-worktree.sh:109], reconciling the
    worktree's Beads git hooks and project config against the installed `bd`
    version. (Beads DB sharing is automatic — worktrees discover the main repo's
    task DB via git's common directory, so there is nothing for `bd doctor` to
@@ -148,8 +149,8 @@ footprint small and its branches short. The conflict-prevention rules from
 
 Each agent otherwise follows the standard PR workflow from its own worktree:
 branch, commit, push, `gh pr create`, wait for CI, squash-merge. The shared
-object store means a merge from `scaffold-alpha` is on `main` for everyone the
-moment it lands.
+object store means a merge from agent `alpha`'s worktree is on `main` for
+everyone the moment it lands.
 
 ## Teardown & harvest
 
@@ -225,7 +226,7 @@ Coming back to parallel work — a context reset, a paused session, the next
 morning — does **not** mean re-running setup. The worktree and its
 `identity.json` persist on disk. Instead:
 
-1. Return to the agent's worktree directory (`../<repo>-<agent>`).
+1. Return to the agent's worktree directory (`.worktrees/<agent>`).
 2. Run **`multi-agent-resume <agent-name>`** (or `single-agent-resume` for the
    non-worktree case). It verifies the worktree environment, syncs with `main`,
    reconciles task status against any PRs merged while you were away, and

package/content/guides/pipeline/index.html

@@ -1392,7 +1392,7 @@ run these <em>over and over</em> while actually writing code.</li>
 <p>The 16 phases are the single source of truth in code: the <code>PHASES</code> constant
 (<span class="fp" data-path="src/types/frontmatter.ts:6">src/types/frontmatter.ts:6</span>) defines every slug, number, and display
 name. Everything in this guide is anchored to it.</p>
-<div class="callout callout-note"><p><strong>89 meta-prompts, not 89 steps you run.</strong> The pipeline directory holds 89 files
+<div class="callout callout-note"><p><strong>90 meta-prompts, not 90 steps you run.</strong> The pipeline directory holds 90 files
 across 16 phase directories, but most projects run only a fraction. Game,
 multi-service, and platform-specific steps are disabled unless an overlay turns
 them on, and many steps are conditional (see <a href="#methodology--depth">Methodology &#x26; depth</a>).</p></div>
@@ -1799,7 +1799,7 @@ how that audit works and what the nine lenses check.</p>
 
 
 
-<table><thead><tr><th>path</th><th>what it holds</th></tr></thead><tbody><tr><td><code>content/pipeline/&#x3C;phase>/*.md</code></td><td>The 89 meta-prompt files, one directory per phase</td></tr><tr><td><code>content/methodology/*.yml</code></td><td>Presets (<code>mvp</code>, <code>custom-defaults</code>, <code>deep</code>) + project-type overlays</td></tr><tr><td><code>content/knowledge/</code></td><td>Domain entries injected into prompts during assembly</td></tr><tr><td><code>src/types/frontmatter.ts</code></td><td>The canonical <code>PHASES</code> constant + frontmatter schema</td></tr><tr><td><code>src/cli/commands/</code></td><td><code>next</code>, <code>run</code>, <code>complete</code>, <code>skip</code>, <code>rework</code>, <code>reset</code>, <code>status</code></td></tr><tr><td><code>.scaffold/state.json</code></td><td>Per-step completion state (planning phases only)</td></tr></tbody></table>
+<table><thead><tr><th>path</th><th>what it holds</th></tr></thead><tbody><tr><td><code>content/pipeline/&#x3C;phase>/*.md</code></td><td>The 90 meta-prompt files, one directory per phase</td></tr><tr><td><code>content/methodology/*.yml</code></td><td>Presets (<code>mvp</code>, <code>custom-defaults</code>, <code>deep</code>) + project-type overlays</td></tr><tr><td><code>content/knowledge/</code></td><td>Domain entries injected into prompts during assembly</td></tr><tr><td><code>src/types/frontmatter.ts</code></td><td>The canonical <code>PHASES</code> constant + frontmatter schema</td></tr><tr><td><code>src/cli/commands/</code></td><td><code>next</code>, <code>run</code>, <code>complete</code>, <code>skip</code>, <code>rework</code>, <code>reset</code>, <code>status</code></td></tr><tr><td><code>.scaffold/state.json</code></td><td>Per-step completion state (planning phases only)</td></tr></tbody></table>
 <p>The phase list, ordering, and slugs are defined exactly once, in <code>PHASES</code>
 (<span class="fp" data-path="src/types/frontmatter.ts:6">src/types/frontmatter.ts:6</span>); every doc, skill, and command resolves
 against it.</p></main>

package/content/guides/pipeline/index.md

@@ -32,7 +32,7 @@ The 16 phases are the single source of truth in code: the `PHASES` constant
 name. Everything in this guide is anchored to it.
 
 :::callout{type=note}
-**89 meta-prompts, not 89 steps you run.** The pipeline directory holds 89 files
+**90 meta-prompts, not 90 steps you run.** The pipeline directory holds 90 files
 across 16 phase directories, but most projects run only a fraction. Game,
 multi-service, and platform-specific steps are disabled unless an overlay turns
 them on, and many steps are conditional (see [Methodology & depth](#methodology--depth)).
@@ -375,7 +375,7 @@ how that audit works and what the nine lenses check.
 
 | path | what it holds |
 | --- | --- |
-| `content/pipeline/<phase>/*.md` | The 89 meta-prompt files, one directory per phase |
+| `content/pipeline/<phase>/*.md` | The 90 meta-prompt files, one directory per phase |
 | `content/methodology/*.yml` | Presets (`mvp`, `custom-defaults`, `deep`) + project-type overlays |
 | `content/knowledge/` | Domain entries injected into prompts during assembly |
 | `src/types/frontmatter.ts` | The canonical `PHASES` constant + frontmatter schema |

package/content/knowledge/execution/worktree-management.md

@@ -17,7 +17,7 @@ Expert knowledge for managing git worktrees to enable parallel multi-agent execu
 
 ### Setup
 
-Use `scripts/setup-agent-worktree.sh <agent-name>` to create a worktree at `../<project>-<agent-name>/`. Each agent gets its own isolated working directory and workspace branch.
+Use `scripts/setup-agent-worktree.sh <agent-name>` to create a worktree at `.worktrees/<agent-name>/` (project-local). Each agent gets its own isolated working directory and workspace branch.
 
 ### Branching Conventions
 
@@ -40,12 +40,12 @@ After all agents finish, remove worktrees and prune stale references. Delete mer
 scripts/setup-agent-worktree.sh agent-1
 
 # This creates:
-#   ../<project>-agent-1/     (working directory)
+#   .worktrees/agent-1/        (working directory, project-local)
 #   Branch: agent-1-workspace  (workspace branch)
 ```
 
 **What the setup script does:**
-1. Creates a new worktree directory adjacent to the main repo
+1. Creates a new worktree directory project-local under `.worktrees/`
 2. Creates a workspace branch for the agent
 3. Sets up the working directory with a clean state
 4. Installs dependencies if a package manager is detected
@@ -154,7 +154,7 @@ git rebase origin/main
 
 ```bash
 # From the main repository (not from inside the worktree)
-git worktree remove ../<project>-agent-1
+git worktree remove .worktrees/agent-1
 ```
 
 **Pruning stale worktree references:**

package/content/knowledge/mcp-server/mcp-authentication.md

@@ -0,0 +1,100 @@
+---
+name: mcp-authentication
+description: MCP authentication patterns — stdio local trust model, OAuth 2.1 for HTTP transports, PKCE, dynamic client registration, API key alternatives, and token validation
+topics: [mcp, authentication, oauth, security, authorization]
+volatility: evolving
+last-reviewed: null
+version-pin: 'MCP spec 2025-11-25; OAuth 2.1 draft-ietf-oauth-v2-1-13'
+sources:
+  - url: https://modelcontextprotocol.io/specification/2025-11-25/basic/authorization
+  - url: https://datatracker.ietf.org/doc/html/draft-ietf-oauth-v2-1-13
+  - url: https://datatracker.ietf.org/doc/html/rfc7591
+  - url: https://www.rfc-editor.org/rfc/rfc8707.html
+---
+
+Authentication in MCP is transport-dependent. stdio servers rely on OS process isolation (no network auth needed). HTTP servers should use OAuth 2.1 for multi-user or multi-tenant scenarios, or simpler API key patterns for internal/single-tenant deployments.
+
+## Summary
+
+**stdio transport**: no network authentication — the server inherits credentials from environment variables and the OS controls process access. **Streamable HTTP transport**: use OAuth 2.1 (per spec) for public or multi-user servers. OAuth flow: client hits protected resource, gets 401 with `WWW-Authenticate`, discovers authorization server via OAuth Protected Resource Metadata, completes OAuth 2.1 with PKCE, presents `Bearer` token on all subsequent requests. For simpler deployments, API keys in headers or environment-injected tokens are practical alternatives. The spec mandates `MCP-Protocol-Version` on HTTP requests and audience validation on tokens.
+
+## Deep Guidance
+
+### stdio: local trust model
+
+The stdio transport requires no network authentication. Trust is established by OS-level process ownership: the client spawns the server as a subprocess, which means both run under the same user account. The server process inherits environment variables from the parent, which is the standard mechanism for passing API keys, database credentials, or access tokens to a local MCP server:
+
+```json
+{
+  "mcpServers": {
+    "my-server": {
+      "command": "npx",
+      "args": ["my-mcp-server"],
+      "env": {
+        "DATABASE_URL": "postgresql://localhost/mydb",
+        "API_KEY": "sk-..."
+      }
+    }
+  }
+}
+```
+
+The spec is explicit: implementations using stdio SHOULD NOT follow the OAuth specification and SHOULD instead retrieve credentials from the environment. Do not add HTTP authentication middleware to a stdio server.
+
+### OAuth 2.1 for HTTP transports
+
+For Streamable HTTP servers accessible over a network, the spec defines an OAuth 2.1 authorization flow. The server acts as an OAuth 2.1 **resource server**; a separate authorization server handles token issuance.
+
+**Discovery flow (updated in 2025-11-25 per RFC 9728 and OIDC Discovery 1.0):**
+1. Client sends an unauthenticated MCP request.
+2. Server MAY respond `401 Unauthorized` with a `WWW-Authenticate` header pointing to the resource server metadata URL; however, the `WWW-Authenticate` header is now OPTIONAL — clients MUST fall back to fetching `/.well-known/oauth-protected-resource` directly if no header is present.
+3. Client fetches `/.well-known/oauth-protected-resource` (RFC 9728) to get the authorization server URL.
+4. Client fetches the authorization server's metadata. Authorization servers that support OpenID Connect SHOULD publish an OIDC Discovery document (`/.well-known/openid-configuration`) in addition to `/.well-known/oauth-authorization-server`.
+5. Client completes the OAuth 2.1 authorization code flow with PKCE. Clients SHOULD use OAuth Client ID Metadata Documents (a recommended client registration mechanism in 2025-11-25) where supported by the authorization server.
+6. Client presents `Authorization: Bearer <token>` on all subsequent requests. Servers MAY issue incremental scope consent via the `WWW-Authenticate` header on subsequent `403` responses.
+
+**PKCE is mandatory** for public clients (MCP clients cannot keep secrets). The authorization server MUST support PKCE. The client generates a `code_verifier` (random string), hashes it to `code_challenge`, includes the challenge in the authorization request, and presents the verifier in the token request.
+
+**Resource parameter** (RFC 8707): clients MUST include a `resource` parameter in both authorization and token requests identifying the MCP server's canonical URI (e.g., `https://mcp.example.com`). This binds tokens to their intended audience and prevents cross-service token reuse.
+
+### Token validation requirements
+
+MCP servers MUST validate every incoming access token:
+- Verify the token is valid and not expired.
+- Verify the token's audience claim identifies this server (matches the server's canonical URI).
+- Reject tokens with `401` if invalid or expired; `403` if the token is valid but lacks required scope.
+
+NEVER accept tokens issued for a different resource. NEVER forward a received token to an upstream API — issue a separate token for each upstream call. Token passthrough is explicitly forbidden by the spec and creates confused deputy vulnerabilities.
+
+### Dynamic client registration
+
+Authorization servers and clients SHOULD support OAuth 2.0 Dynamic Client Registration (RFC 7591). As of 2025-11-25, OAuth Client ID Metadata Documents are the recommended client registration mechanism — they allow clients to declare their identity via a URL rather than requiring a registration round-trip. Without dynamic registration support, MCP clients must be pre-registered with every authorization server, which creates friction for discovering and connecting to new servers. Dynamic registration lets a client auto-register on first connection:
+
+```
+POST /register
+{ "client_name": "Claude Desktop", "redirect_uris": ["http://localhost:57842/callback"] }
+→ { "client_id": "abc123", ... }
+```
+
+If the authorization server does not support dynamic registration, the client must hardcode a client ID or present a UI for manual credential entry.
+
+### Simpler alternatives for private/internal deployments
+
+For servers used only within a controlled environment (team tool, internal service), full OAuth is often unnecessary overhead. Practical alternatives:
+
+**API key in header**: The client includes a static API key in a custom header or as a Bearer token. The server validates it against a stored secret. Simple, easy to rotate, no token exchange flow.
+
+**Mutual TLS**: Suitable for service-to-service scenarios where both sides have certificates. The TLS handshake authenticates both parties.
+
+**Reverse proxy with auth**: Run the MCP server behind nginx/Caddy/Cloudflare with authentication handled at the proxy layer. The server itself trusts all proxied connections.
+
+**Network isolation**: For truly internal deployments, rely on network controls (VPN, private subnet, firewall rules) and skip application-layer auth. Acceptable only when the network boundary is the full security boundary.
+
+### Security hardening checklist
+
+- Validate the `Origin` header on all Streamable HTTP connections to prevent DNS rebinding attacks.
+- Use HTTPS for all HTTP transport connections (required by OAuth 2.1 for authorization server endpoints and redirect URIs).
+- Bind local HTTP servers to 127.0.0.1, not 0.0.0.0.
+- Rotate API keys and tokens regularly; issue short-lived access tokens.
+- Log all authentication failures with enough context to diagnose attacks.
+- Do not embed credentials in resource URIs (they appear in logs and referrer headers).