@bevel-software/platform-core-backend 0.22.0 → 0.24.0

package/dist/modules/workspace/workspace.tools.js

@@ -1,16 +1,17 @@
 import { spawn } from 'node:child_process';
 import nodeFs from 'node:fs/promises';
 import { join } from 'node:path';
+import AdmZip from 'adm-zip';
 import { ToolError } from '../tool-helpers/tool.contract.js';
 import { BRANCH_INPUT, toolDef } from '../tool-helpers/tool-def.js';
-import { recordOntologyRead, assertOntologyWriteAllowed, assertShellAllowedWithinOntology, ONTOLOGY_BOUNDARY_NOTE, SESSION_ID_INPUT, } from './session-ontology.gate.js';
+import { notifyAgentRead, assertAgentWriteAllowed, SESSION_ID_INPUT, } from './agent-access.gate.js';
 import { requireInternalSource, requireExternalSource } from '../tool-auth/tool-auth.middleware.js';
 import { workspaceIdForBranch } from '../../shared/workspace-id.js';
-import { assertBranchProvided } from '../../shared/domain-errors.js';
+import { assertBranchProvided, GitInternalsError, WorkflowValidationError } from '../../shared/domain-errors.js';
 // Leaf-level shared primitive (same exception `workspace.service.ts` already
 // relies on) — not a workflow service, so this stays inside the module boundary.
 import { assertValidBranchName } from '../kb-fs/branch-name.js';
-import { assertInsideRepo, assertRepoRootNameFreeArgs, normalizePathArgs } from '../kb-fs/repo-path.js';
+import { assertInsideRepo, assertRepoRootNameFree, assertRepoRootNameFreeArgs, isInsideRepo, normalizePathArgs, } from '../kb-fs/repo-path.js';
 import { GitGuardedFilesystem } from '../kb-fs/git-guarded-filesystem.js';
 import { assertNoGitInternalsSegment, assertNotGitInternals, hasGitInternalsSegment } from '../../shared/git-internals.js';
 import { isRolesYamlPath } from '../access-model/roles-yaml-guard.js';
@@ -23,14 +24,16 @@ import { fileTypeOf, needsContent } from './file-readers/content-mode.js';
 import { createFileReaderRegistry } from './file-readers/file-reader.registry.js';
 import { DocumentReader } from './file-readers/document-reader.js';
 import { mcpImageResult } from '@bevel-software/platform-mcp-core';
-import { LEGACY_AGENTS_FILE, folderPlaceholderPath, isFolderPlaceholder, isPlatformFile, isPlatformFolder, platformFileCreationRefusal, platformFileNames, platformFileRefusal, platformFolderRefusal, entryExistsMessage, } from '@bevel-software/platform-shared';
+import { folderPlaceholderPath, isFolderPlaceholder, isPlatformFile, isPlatformFolder, platformFileCreationRefusal, platformFileRefusal, platformFileUploadRefusal, platformFolderRefusal, entryExistsMessage, } from '@bevel-software/platform-shared';
 import { AccessDeniedError } from '../access-model/access-errors.js';
 import { removeEmptyDirs } from './empty-dirs.js';
-import { PROPOSAL_ROUTE_NOTE, rethrowAsWriteDenial } from './write-denial.js';
+import { rethrowAsWriteDenial } from './write-denial.js';
+import { sharedRulesPointer } from '../agent-instructions/shared-file-rules.js';
 import { notFound, orDeclaredNotFound, orNotFound } from './not-found.js';
 import { logger } from '../../shared/logging.js';
 import { printable } from '../../shared/printable.js';
 import { DestinationTakenError, inspectDestination } from '../../shared/rename-no-replace.js';
+import { isSymlinkZipEntry, isZipNoiseEntry, readZipEntry, zipEntryName, zipEntryNameRefusal, zipEntrySegments, } from './zip-entry-rules.js';
 const log = logger('workspace-tools');
 /** How many files `file_stat` counts under a folder before it stops and says so. */
 const DESCENDANTS_CAP = 10_000;
@@ -122,53 +125,23 @@ async function keepFolderOf(fs, ctx, branch, removedPath, kbDirName) {
         throw err;
     }
 }
-/**
- * Appended (centrally, in `mount`) to EVERY workspace tool description. The
- * platform's managed agent guide sits at the workspace root and documents the
- * conventions of that knowledge base; agents (ours and external) should consult
- * it before touching files. It rides on every entrypoint — reads (grep/
- * list_files/file_stat) included — because any of them can be a session's first
- * touch.
- *
- * `CLAUDE.md` is named as a fallback because knowledge bases seeded before the
- * rename still carry one, and the seeder never deletes a file it did not
- * expect. Naming both means an agent finds the conventions either way, instead
- * of reading none because it looked for the newer name and stopped.
- *
- * WHEN THE GUIDE HAS BEEN RENAMED the sentence names two files, ours first. The
- * second is the organisation's OWN `AGENTS.md`, which on such a deployment is
- * ordinary content the platform never touches — and which no harness reads for a
- * remote agent, because a remote agent has no checkout. Telling it to read both
- * is the only way the conventions the customer actually wrote reach the agent
- * working in their knowledge base. Under the default name the wording collapses
- * to the one file it has always named.
- *
- * A FUNCTION of the layout, called when a description is built: the name is a
- * deployment setting, and a module-scope string would snapshot the default.
- */
-function kbConventionsNote(layout) {
-    const agentsFile = layout.agentsFile ?? LEGACY_AGENTS_FILE;
-    if (agentsFile === LEGACY_AGENTS_FILE) {
-        return ' Before your first read or change in a workspace, read `AGENTS.md` at the KB root — or `CLAUDE.md` on a knowledge base seeded before it was renamed — if either exists: it holds the author\'s conventions for this knowledge base, and you should follow them.';
-    }
-    return (` Before your first read or change in a workspace, read \`${agentsFile}\` at the KB root, then ` +
-        '`AGENTS.md` if it also exists (the organisation\'s own conventions) — or `CLAUDE.md` on a knowledge base seeded before it was renamed: together they hold the conventions for this knowledge base, and you should follow them.');
-}
-/** The platform files as a tool description lists them — the guide under its own name. */
-function platformFileList(layout) {
-    return platformFileNames(layout)
-        .map((name) => `\`${name}\``)
-        .join(', ');
-}
 const int = (description) => ({ type: 'integer', description });
 const str = (description) => ({ type: 'string', description });
 /**
- * Where pictures go, on the two tools that write pages. An agent in core cannot
- * upload bytes yet (TODOS.md), but it can write the page with the link a person
- * will satisfy, and this sentence is what keeps every page it writes on the
- * README's convention: images beside the page, linked relatively.
+ * The upload route, named on every tool that takes content as a JSON string.
+ *
+ * ONE sentence, and the tools' own: it is what stops the three failures the
+ * route was built for. An agent landing 27 files read each one and typed it
+ * out again as a tool argument: a 37 KB write was truncated mid-answer, a page
+ * of regex backslashes failed to parse as a JSON parameter, and a PNG could not
+ * be sent at all. None of that is discoverable from a refusal — a truncated
+ * write reports success — so the tools that invite it name where the bytes
+ * should go instead, in the description itself, for a client that reads
+ * nothing else. WHY, and how the route is used, is one of the shared rules
+ * (`agent-instructions/shared-file-rules.ts`): said in full on three
+ * descriptions it took each of them past the length a client cuts at.
  */
-const IMAGE_CONVENTION_NOTE = ' Images: keep them in an `assets/` folder next to the page that uses them and link them with a relative path, e.g. `![Approval screen](./assets/approval-screen.png)`; the page renders them inline.';
+const UPLOAD_ROUTE_NOTE = ' Large, escape-heavy or binary content does not go through here: use `request_file_upload` + `apply_file_upload`.';
 /**
  * A path input that names the clone folder, and says what happens when it does
  * not. The tools are rooted at the WORKSPACE dir, one level above the git clone,
@@ -202,6 +175,9 @@ const RESERVED_ROOT_NAME_TARGETS = {
     copy_file: ['dest'],
     move_file: ['dest'],
     unzip: ['destination'],
+    // The folder the upload lands in. Each of its own paths is checked again
+    // inside the handler — an archive chooses its entry names, not the caller.
+    apply_file_upload: ['destination'],
 };
 function asText(content) {
     return typeof content === 'string' ? content : content.toString('utf8');
@@ -219,14 +195,6 @@ function asBytes(content) {
  * `read_file`, which extracts unbudgeted) will cover the rest.
  */
 const UNCACHED_DOCS_PER_GREP = 20;
-/**
- * THE binary capability contract, stated once and appended (in `mount`) to
- * every file tool's description — which is also what `tools_info` returns.
- * The split it states is enforced by the reader registry: the text tools
- * refuse what their reader marks not `textEditable` (and binary content under
- * any name) with a `binary_not_writable` refusal; the byte tools never look.
- */
-export const CONTENT_RULE = ' Content rule (the same on every file tool): read_file returns text for text files and extracted text for documents (.docx/.pptx/.xlsx/.odt/.odp/.ods/.pdf, .eml/.msg); write_file, write_files and edit_file accept TEXT only — they refuse documents, images, archives and other binary files (legacy .doc/.ppt/.xls included) with kind `binary_not_writable`, naming the file\'s kind and the tool to use instead; copy_file, move_file, delete_file and unzip act on bytes of any kind; new binary content arrives through upload (`request_upload_token` + `apply_upload` where offered, otherwise Upload in the app). file_stat reports `contentMode` (`text` | `document` | `binary`) so you can decide before acting.';
 /** What a `binary_not_writable` refusal points to, in the order to try them. */
 const BINARY_USE_INSTEAD = ['upload', 'copy_file', 'move_file'];
 /**
@@ -237,7 +205,7 @@ const BINARY_USE_INSTEAD = ['upload', 'copy_file', 'move_file'];
  */
 function binaryNotWritable(fileKind, explanation) {
     return new ToolError(`${explanation} [binary_not_writable: this file's kind is ${fileKind}; write_file, write_files and edit_file accept text only. ` +
-        'Use upload for new bytes (`request_upload_token` + `apply_upload` where offered, otherwise Upload in the app), ' +
+        'Use upload for new bytes (`request_file_upload` + `apply_file_upload`, or Upload in the app), ' +
         'or copy_file / move_file to place bytes that are already in the workspace.]', 415, { kind: 'binary_not_writable', fileKind, useInstead: [...BINARY_USE_INSTEAD] });
 }
 /** The generic why, for a reader without format-specific refusal copy. */
@@ -314,11 +282,6 @@ const WRITE_MODE_INPUT = {
         'holds something; `overwrite` replaces what is there, and creates the file when there is nothing; `update` replaces an ' +
         'EXISTING file and refuses (`missing`) a path that holds nothing.',
 };
-/** The same three modes, said once, for both tool descriptions. */
-const WRITE_MODE_NOTE = ' `mode` decides what may happen at a path and DEFAULTS TO `create`: `create` writes a new file and refuses a path that ' +
-    'already exists (`exists`, with the path — pass `mode: overwrite` to replace it), `overwrite` replaces what is there ' +
-    '(creating it if there is nothing), `update` replaces an existing file and refuses a path that does not exist (`missing`). ' +
-    'A refused path is left exactly as it was.';
 /** The refusal `create` gives on a path that already holds something. */
 function pathExists(path) {
     return new ToolError(`"${displayPath(path)}" already exists — pass mode: overwrite to replace it, or write to a different path.`, 409, { code: 'exists', path });
@@ -342,6 +305,144 @@ function decideWrite(mode, path, exists) {
         return 'updated';
     return exists ? 'replaced' : 'created';
 }
+/**
+ * How many of an upload's paths the answer NAMES before it stops and says how
+ * many there were. A 300-file zip's full outcome list is pages of text an agent
+ * pays for on every call; 25 is enough to see the shape of what happened, and
+ * `total` plus `truncated` say that there is more. `all: true` asks for the
+ * rest, for a caller that really does have to read each one.
+ */
+const APPLY_ANSWER_CAP = 25;
+/**
+ * How many entries of one uploaded archive are landed, and how many bytes of
+ * uncompressed content in total.
+ *
+ * Tighter than `unzip`'s own caps on purpose. An apply lands its whole set as
+ * ONE commit, which means every entry's bytes are held in memory at once —
+ * the property that makes the commit atomic is the one that makes a zip bomb
+ * expensive. The upload itself is already bounded by the deployment's upload
+ * limit; these bound what that upload is allowed to expand into.
+ */
+const APPLY_MAX_ENTRIES = 5_000;
+const APPLY_MAX_TOTAL_BYTES = 128 * 1024 * 1024; // 128 MB uncompressed
+/**
+ * Turn a stored upload into one planned path per file.
+ *
+ * A single file is one path: the destination plus the name it was sent with.
+ * A zip is one path per member, with the member's folder structure kept under
+ * the destination — judged by the same entry rules `unzip` applies
+ * (`zip-entry-rules.ts`), plus one `unzip` does not have: an entry that is a
+ * symbolic LINK is refused outright. A zip stores a link as a member whose
+ * bytes are its target text, so a reader that ignored the mode bits would
+ * write that text out as a file — content nobody sent, under a name that was
+ * meant to point elsewhere.
+ */
+/** The refusal an entry gets when the archive would expand past what one commit lands. */
+function tooLargeToApply() {
+    return `This archive expands past the ${APPLY_MAX_TOTAL_BYTES} byte total the apply lands in one commit; this entry was not applied.`;
+}
+async function planUpload(upload, destination, kbDirName) {
+    const bytes = await nodeFs.readFile(upload.absolutePath);
+    if (upload.kind !== 'zip') {
+        return [{ path: `${destination}/${upload.filename}`, content: bytes }];
+    }
+    let zip;
+    try {
+        zip = new AdmZip(bytes);
+    }
+    catch (err) {
+        throw new ToolError(`"${upload.filename}" could not be opened as a .zip archive: ${err instanceof Error ? err.message : String(err)}`, 422, { code: 'unreadable_archive' });
+    }
+    const planned = [];
+    let seen = 0;
+    let totalBytes = 0;
+    for (const entry of zip.getEntries()) {
+        const rawName = zipEntryName(entry.entryName);
+        if (isZipNoiseEntry(rawName))
+            continue;
+        if (seen >= APPLY_MAX_ENTRIES) {
+            planned.push({
+                path: rawName || '(empty)',
+                error: 'too_many_entries',
+                message: `This archive holds more than ${APPLY_MAX_ENTRIES} entries; the rest were not applied.`,
+            });
+            continue;
+        }
+        seen++;
+        const nameRefusal = zipEntryNameRefusal(rawName);
+        if (nameRefusal !== null) {
+            planned.push({ path: rawName || '(empty)', error: 'invalid_entry', message: nameRefusal });
+            continue;
+        }
+        if (isSymlinkZipEntry(entry)) {
+            planned.push({
+                path: rawName,
+                error: 'link',
+                message: `"${rawName}" is a symbolic link, not a file; an upload lands files, never links.`,
+            });
+            continue;
+        }
+        // A folder comes into being with the files under it (the write path mkdirs
+        // each parent), so a directory member has nothing of its own to land.
+        if (entry.isDirectory)
+            continue;
+        const segments = zipEntrySegments(rawName);
+        const target = [destination, ...segments].join('/');
+        // Belt and braces: `zipEntryNameRefusal` already refuses a `..` segment
+        // and a root-anchored name, so nothing should reach here that climbs out.
+        // The check stays because the cost of being wrong about that is bytes
+        // landing outside the folder the caller named.
+        if (!target.startsWith(`${destination}/`) || !isInsideRepo(target, kbDirName)) {
+            planned.push({ path: rawName, error: 'invalid_entry', message: 'Path escapes destination' });
+            continue;
+        }
+        // Through the one bounded reader `unzip` uses too, capped at what is left
+        // of the budget: a deflate stream can expand a thousandfold, and the
+        // header's declared size is the archive's claim, not a fact — an entry
+        // declaring ZERO would otherwise be inflated with no cap at all (see
+        // `readZipEntry`). A read that fails is this entry's outcome and no more.
+        const read = readZipEntry(entry, APPLY_MAX_TOTAL_BYTES - totalBytes);
+        if (!read.ok) {
+            planned.push(read.reason === 'too_large'
+                ? { path: rawName, error: 'too_large', message: tooLargeToApply() }
+                : { path: rawName, error: 'unreadable_entry', message: `"${rawName}" could not be read: ${read.detail}.` });
+            continue;
+        }
+        totalBytes += read.data.byteLength;
+        planned.push({ path: target, content: read.data });
+    }
+    return planned;
+}
+/**
+ * Record on `entry` that this path was refused, saying what the gate that
+ * refused it said. Four kinds of refusal count as one path's outcome: a
+ * typed tool refusal (`exists`, `platform_file`, the mode gate), a permission
+ * refusal (the caller may not write this path, where the DESTINATION was
+ * writable), the git folder in any spelling, and a path-shape refusal from the
+ * repository rules. Anything else
+ * is not a verdict about this path — it is a gate failing — so it travels on
+ * and the whole apply fails loudly, exactly as it does in `write_files`.
+ */
+function refuseEntry(entry, err) {
+    entry.outcome = 'refused';
+    if (err instanceof ToolError) {
+        const details = (err.details ?? {});
+        entry.error = details.code ?? details.kind ?? 'refused';
+        entry.message = err.message;
+        return;
+    }
+    if (err instanceof AccessDeniedError) {
+        entry.error = 'write-denied';
+        entry.message = err.message;
+        return;
+    }
+    if (err instanceof GitInternalsError || err instanceof WorkflowValidationError) {
+        entry.error = err.payload?.kind ?? 'refused';
+        entry.message = err.message;
+        return;
+    }
+    throw err;
+}
 /** The three modes, as a set the handler can check a raw argument against. */
 const WRITE_MODES = ['create', 'overwrite', 'update'];
 /**
@@ -431,7 +532,7 @@ async function searchRootKind(fs, path) {
     }
 }
 /** JS grep over the workspace tree (read methods only) — bounded by match + depth caps. */
-async function grepWalk(fs, dir, re, out, max, depth, gate, recordOntologyRead, docs) {
+async function grepWalk(fs, dir, re, out, max, depth, gate, notifyRead, docs) {
     if (out.length >= max || depth > 12)
         return;
     let entries;
@@ -453,13 +554,13 @@ async function grepWalk(fs, dir, re, out, max, depth, gate, recordOntologyRead,
             continue;
         const p = dir ? `${dir}/${e.name}` : e.name;
         if (e.type === 'directory') {
-            await grepWalk(fs, p, re, out, max, depth + 1, gate, recordOntologyRead, docs);
+            await grepWalk(fs, p, re, out, max, depth + 1, gate, notifyRead, docs);
         }
         else {
-            // Opening a file under a named ontology is a read of that ontology — even
-            // for a root-level grep that resolves to a neutral root. Record it so a
-            // cross-ontology grep poisons later writes (closes the read-leak).
-            await recordOntologyRead(p);
+            // Opening a file is a read of it, even when the walk started at a root
+            // the read hook was already told about — so every file the walk opens
+            // reaches the hook by name (closes the read-leak).
+            await notifyRead(p);
             // A file the walk cannot read is silently skipped: one unreadable entry
             // must not fail a search over the whole tree.
             try {
@@ -489,6 +590,17 @@ const BATCH_SAVE_WARNINGS_OUTPUT = {
         'The writes still happened.',
     items: { type: 'object' },
 };
+/**
+ * The `sessionId` property inside a BUILT tool def's input schema, or
+ * `undefined` for a tool that declares none. `toolDef` wraps the flat inputs
+ * under `body` and copies the schema it is given, so a note registered after
+ * the tools were built has to be written here rather than onto the shared
+ * `SESSION_ID_INPUT` constant.
+ */
+function sessionIdInputOf(def) {
+    const inputs = def.inputs;
+    return inputs?.properties?.body?.properties?.sessionId;
+}
 /**
  * Workspace domain tools: the file primitives (replacing Mastra's auto-injected
  * Workspace tools) + unzip. Most just re-expose the SAME `LocalFilesystem`
@@ -498,7 +610,7 @@ const BATCH_SAVE_WARNINGS_OUTPUT = {
  * method), so they're implemented here. File ops are `both`; `execute_command`
  * is INTERNAL-only (arbitrary shell as the caller is too dangerous to expose).
  */
-export function registerWorkspaceTools(registry, router, toolAuth, toolHandler, spillStore, docExtract, accessControl, kb, sessionOntologyGate, writePolicy, sessionSink, 
+export function registerWorkspaceTools(registry, router, toolAuth, toolHandler, spillStore, docExtract, accessControl, kb, agentAccessGate, writePolicy, sessionSink, 
 /**
  * Save-time skill check (see `AllowedToolsChecker`): a write to a SKILL.md
  * returns `warnings` for `allowed-tools` entries naming no visible tool.
@@ -511,7 +623,16 @@ skillSaveCheck,
  * would be made on. Optional so tool harnesses need not wire it; the read
  * verdict alone then decides, which differs only at a root.
  */
-changeGate) {
+changeGate, 
+/**
+ * The upload-token store behind `request_file_upload` / `apply_file_upload`
+ * — the route an agent lands bytes by, without their content passing
+ * through the model. Optional for the same reason the two above are: a tool
+ * harness that is about the file primitives need not stand one up. Every
+ * real composition wires it (`create-core-server.ts`), and without it the
+ * two tools are not mounted at all rather than mounted and broken.
+ */
+uploads) {
     const { kbDirName } = kb;
     /**
      * The one extension→reader registry every read-shaped decision routes
@@ -582,7 +703,7 @@ changeGate) {
      * Every spelling first, then the resolved form against the branch's
      * workspace, so a link into the folder is refused the same way. The resolved
      * check only runs on a branch that is already cloned: bootstrapping a clone
-     * here would happen before the handler's access and ontology gates. A branch
+     * here would happen before the handler's access and agent-access gates. A branch
      * not cloned yet (or that does not resolve) is left to the handler; the
      * filesystem refuses again underneath regardless.
      */
@@ -605,7 +726,7 @@ changeGate) {
      * The branch's workspace root, to judge a spelling against what is on disk
      * — or null when there is nothing to judge it against yet. Only a branch
      * ALREADY cloned is used: bootstrapping one here would clone before the
-     * handler's access and ontology gates have had their say.
+     * handler's access and agent-access gates have had their say.
      */
     const gitCheckRootFor = async (args, ctx) => {
         if (typeof args.branch !== 'string' || args.branch === '')
@@ -672,6 +793,112 @@ changeGate) {
         ]);
         return { read, write, download, owner };
     };
+    /** Whether any one of the caller's four verdicts differs between the two sides of a preview. */
+    const verbsDiffer = (before, after) => Object.keys(before).some((v) => before[v] !== after[v]);
+    /**
+     * Why `copy_file` will not take a folder. One sentence, said by the dry
+     * run and by the call itself, so the preflight and the execution never
+     * disagree — the rule this whole section is built on.
+     */
+    const folderCopyRefusal = (src) => `"${src}" is a folder; copy_file copies one file. Copy its files one by one, or move the folder with move_file.`;
+    /**
+     * The caller's verdicts at `dest` as they will be once `src` has been
+     * moved (or, with `sourceRemains`, copied) there — the `after` half of a
+     * move's or copy's preview.
+     *
+     * `accessAt(dest)` is the wrong answer to that question for a folder: the
+     * destination on disk has neither the folder nor the `access.md` files it
+     * carries, so it describes the destination's PARENT. A rename of a folder
+     * that names the caller owner in its own `access.md` therefore warned
+     * about losing owner access the move was about to hand straight back, and
+     * a warning that is wrong is a warning people learn to click through.
+     *
+     * Preview only, like everything else in this section: it answers what the
+     * caller WILL have, never whether they may do it. The write verdicts that
+     * gate the move are `writeBlocked` and the lock gate, both of which read
+     * the tree as it is.
+     */
+    const accessAfter = async (branch, ctx, src, dest, opts) => {
+        const from = toKbRelative(src, kbDirName);
+        const to = toKbRelative(dest, kbDirName);
+        // Outside the repository there are no rules to carry, and none to land
+        // among — the same answer `accessAt` gives for such a path.
+        if (from === null || to === null)
+            return accessAt(branch, ctx, dest);
+        return accessControl.previewAccessAfterRelocation(workspaceIdForBranch(branch), ctx.user.email, from, to, opts);
+    };
+    /**
+     * What `copy_file`'s dry run answers: the same impact shape `move_file`
+     * previews, over a copy's own rules.
+     *
+     * A copy LEAVES the source where it is, so the rules it carries are
+     * duplicated rather than relocated (`sourceRemains`) — otherwise the two
+     * previews ask the same question. The order of the refusals is `copy_file`'s
+     * own and is load-bearing: the write verdict on the destination outranks
+     * "that name is taken", because a caller who may not write a folder must
+     * not learn what is in it from a refusal.
+     *
+     * A folder source is reported as the refusal it is. `copy_file` copies one
+     * file; the preview says so rather than promising a copy that would fail,
+     * and still answers `access.after` for the folder it was asked about.
+     *
+     * NOTHING is probed on disk until the write verdict on the destination has
+     * been taken — not the destination, and not the source either, which is the
+     * order the call itself keeps at length: a caller who may not write there
+     * gets the same refusal whether the source is a file, a folder, or missing
+     * altogether. Probing the source first put a 404 in front of that 403 and
+     * handed a denied caller the source's kind and its file count. So a refused
+     * preview answers `allowed: false` with the sentence and no `kind` or
+     * `descendants`: those are the half of the impact the caller has to have
+     * earned. The two `access` sides are the caller's own four verbs and tell
+     * them nothing they could not ask `file_stat` for.
+     */
+    const copyImpact = async (branch, ctx, src, dest) => {
+        const [before, after, blocked] = await Promise.all([
+            accessAt(branch, ctx, src),
+            accessAfter(branch, ctx, src, dest, { sourceRemains: true }),
+            writeBlocked(branch, ctx, [dest]),
+        ]);
+        const access = { before, after };
+        const accessChanges = verbsDiffer(before, after);
+        if (blocked.length > 0) {
+            return {
+                src,
+                dest,
+                access,
+                accessChanges,
+                allowed: false,
+                reason: `You may not write "${dest}", so the copy cannot run.`,
+                dryRun: true,
+                copied: false,
+            };
+        }
+        const fs = await ctx.getFilesystem(branch);
+        const kind = await kindOf(fs, src);
+        if (kind === null)
+            throw notFound(src, 'Nothing to copy');
+        const srcFiles = kind === 'folder' ? (await filesUnder(fs, src)).files : [src];
+        const occupiedBy = await existingAt(await workspaceRoot(branch, ctx), dest);
+        const reason = occupiedBy !== null
+            ? entryExistsMessage(occupiedBy, dest)
+            : kind === 'folder'
+                ? folderCopyRefusal(src)
+                : undefined;
+        return {
+            src,
+            dest,
+            kind,
+            // The placeholder travels with its folder, but it is never content —
+            // counted as `move_file` counts it.
+            descendants: srcFiles.filter((f) => !isFolderPlaceholder(f)).length,
+            access,
+            accessChanges,
+            allowed: reason === undefined,
+            ...(reason !== undefined ? { reason } : {}),
+            dryRun: true,
+            copied: false,
+        };
+    };
     /**
      * The paths among `paths` the caller may NOT write, judged exactly as the
      * lock gate judges them (`WorkflowService.acquireLock`): on a protected
@@ -947,10 +1174,14 @@ changeGate) {
     const linkRefusal = (path) => `"${path}" is a symbolic link; the agent tools never follow or remove links.`;
     const mount = (spec) => {
         const path = `/api/agent/tools/${spec.name}`;
-        // Every workspace entrypoint carries the agent-guide reminder, every file
-        // tool the one content rule, and every tool a permission can refuse the
-        // proposal route — appended once here so no tool (especially the
-        // read-only ones a session hits first) can miss them.
+        // Every description ends with ONE sentence pointing at the rules these
+        // tools share — the content rule, the agent guide, the write modes, the
+        // dry-run protocol, the proposal route. They used to be appended here in
+        // FULL, which made a description several thousand characters of text the
+        // agent had already read on the tool above, and clients cut a long
+        // description from the END, where what is specific to the tool sits. The
+        // rules themselves are in the handshake instructions and in the managed
+        // guide (see `shared-file-rules.ts`), stated once and from one text.
         // Whether a call to this tool MUST name a branch, read off the tool's own
         // declaration rather than assumed of the family. Every tool mounted here
         // requires `branch` today; keying on the schema means a tool that declares
@@ -958,9 +1189,8 @@ changeGate) {
         // own route) is not handed a refusal it never asked for.
         const requiresBranch = (spec.inputs.required ?? []).includes('branch');
         const describe = () => (typeof spec.description === 'function' ? spec.description() : spec.description) +
-            (spec.proposable ? PROPOSAL_ROUTE_NOTE : '') +
-            (spec.fileTool === false ? '' : CONTENT_RULE) +
-            kbConventionsNote(kb.layout);
+            (spec.gated ? agentAccessGate.notes.gatedToolNote() : '') +
+            sharedRulesPointer(kb.layout);
         const def = toolDef({
             name: spec.name,
             description: describe(),
@@ -972,16 +1202,33 @@ changeGate) {
         registry.registerInternalTool(def);
         if (!spec.internalOnly)
             registry.registerExternalTool(def);
-        // The catalog FOLLOWS the layout. The conventions reminder above names the
-        // guide, and several descriptions name it again as a platform file, so the
-        // save that completes first-run setup — which applies the names the admin
-        // just chose, in that same request, without a restart — must be able to
-        // move the text with them. Rewritten in place: the registry holds this
-        // object, both surfaces hold the same one, and re-registering would be a
-        // duplicate name.
-        kb.onLayoutApplied(() => {
+        /**
+         * What the agent reads about this tool, rebuilt from whatever is in effect
+         * NOW: the layout's names and the notes the deployment registered.
+         *
+         * The catalog FOLLOWS the layout. The conventions reminder above names the
+         * guide, and several descriptions name it again as a platform file, so the
+         * save that completes first-run setup — which applies the names the admin
+         * just chose, in that same request, without a restart — must be able to
+         * move the text with them. Rewritten in place: the registry holds this
+         * object, both surfaces hold the same one, and re-registering would be a
+         * duplicate name. The `sessionId` input is rewritten on the DEF rather
+         * than on `SESSION_ID_INPUT`, because `toolDef` copies the schema it is
+         * given.
+         */
+        const redescribe = () => {
             def.description = describe();
-        });
+            const sessionId = sessionIdInputOf(def);
+            if (sessionId)
+                sessionId.description = agentAccessGate.notes.sessionIdDescription();
+        };
+        // Once for a note registered BEFORE the tools were mounted (the `sessionId`
+        // input is copied by `toolDef`, so it carries the bare default until this
+        // runs), and then on every later change: a note may be registered AFTER
+        // the mount, from the tool-surface hook an overlay registers on.
+        redescribe();
+        kb.onLayoutApplied(redescribe);
+        agentAccessGate.notes.onChange(redescribe);
         // Internal-only tools (e.g. `execute_command`) keep their route mounted —
         // our agent calls it over the same loopback — but gate it to internal-source
         // callers so an external connection key can't invoke it by name.
@@ -1039,22 +1286,20 @@ changeGate) {
         }, { write: spec.write }));
     };
     // ── session bootstrap (external agents) ─────────────────────────────────
-    // Every read/write tool below scopes the ontology-session boundary off a
-    // `sessionId`. The in-process agent carries its thread id, but an external
-    // agent has no ambient run id and so cannot satisfy the gate until it has
-    // one. This mints that id up front (called ONCE); the MCP proxy then threads
-    // it onto every later gated call via its sessionId-output continuity
+    // Every read/write tool below takes a `sessionId`: the conversation the
+    // call belongs to, which is what a deployment's hooks scope their rule to.
+    // The in-process agent carries its thread id, but an external agent has no
+    // ambient run id, so this mints one up front (called ONCE); the MCP proxy
+    // then threads it onto every later call via its sessionId-output continuity
     // convention. EXTERNAL-ONLY (not registered internal): the in-process agent
     // already supplies its session id and ignores any body value.
     //
     // WHAT the minted id is backed by is the `ISessionSink` port's business
     // (session-sink.ts). In the enterprise app it is a REAL chat-thread id, so
-    // the SAME id works end to end: KB reads scope the ontology boundary under
-    // it, AND `ask` accepts it (its sessionId IS a chat thread, resolved via
-    // getThread) — that unification is what stops a caller reading from one
-    // ontology and then having `ask` write into another. In a core-only
-    // deployment (no chat/ask) the default sink mints a bare id, which is all
-    // the ontology gate needs.
+    // the SAME id works end to end: the file tools take it AND `ask` accepts it
+    // (its sessionId IS a chat thread, resolved via getThread), so a run's reads
+    // and its questions are one conversation rather than two. In a core-only
+    // deployment (no chat/ask) the default sink mints a bare id.
     //
     // The description tells the caller that retrying is safe, and that is a
     // property of the sink rather than a promise this route makes on its own:
@@ -1066,7 +1311,7 @@ changeGate) {
     // transport hiccup on its first call as an unrecoverable start.
     const startSessionDef = toolDef({
         name: 'start_session',
-        description: 'Mint the KnowledgeBase session id this run needs to read or write the knowledge ontologies. Call this ONCE, before any other KnowledgeBase tool, and only once per run — every gated tool needs the `sessionId` it returns to enforce the one-ontology-per-conversation boundary, and minting a new id mid-run resets that boundary. The id is also a chat session in the app, so you can hand the SAME id to the `ask` tool: reads and ask then share one ontology boundary. Pass the returned id explicitly as `sessionId` on every subsequent KnowledgeBase tool call (direct MCP calls and inside `call_tool_chain` alike). RETRYING IS SAFE: a call that fails created nothing, so retry it — there is no half-made session to clean up. If a retry lands after a success you simply hold two independent ids, which is harmless: keep passing the one id you have already used for the rest of the run and ignore the other. Returns `{ sessionId }`.',
+        description: 'Mint the id of this conversation, which the KnowledgeBase tools take as `sessionId`. Call this ONCE, at the start of your work and only once per run — minting a new id mid-run starts a second conversation as far as the server is concerned. The id is also a chat session in the app, so you can hand the SAME id to the `ask` tool: your reads and your questions are then one conversation. Pass the returned id explicitly as `sessionId` on every subsequent KnowledgeBase tool call (direct MCP calls and inside `call_tool_chain` alike). RETRYING IS SAFE: a call that fails created nothing, so retry it — there is no half-made session to clean up. If a retry lands after a success you simply hold two independent ids, which is harmless: keep passing the one id you have already used for the rest of the run and ignore the other. Returns `{ sessionId }`.',
         path: '/api/agent/tools/start_session',
         inputs: { type: 'object', properties: {}, additionalProperties: false },
         outputs: {
@@ -1078,10 +1323,10 @@ changeGate) {
     });
     registry.registerExternalTool(startSessionDef);
     // Mint the session id via the sink and return it (see comment above: one id
-    // spans start_session -> reads -> ask, closing the ontology-pollution gap).
+    // spans start_session -> reads -> ask).
     router.post('/agent/tools/start_session', toolAuth, 
     // External-only: an internal token already carries its run's sessionId, so
-    // minting a new thread mid-run would reset the ontology boundary. Note
+    // minting a new thread mid-run would split one run in two. Note
     // "external" includes the MCP proxy's `externalProxy` loopback tokens
     // (OAuth/JWT MCP sessions) — the verifier resolves those to
     // `source: 'external'`, and one such session may legitimately mint several
@@ -1093,8 +1338,14 @@ changeGate) {
     // ── reads ──────────────────────────────────────────────────────────────
     mount({
         name: 'read_file',
-        description: 'Read a workspace file as text. Returns `{ path, content }`. Images (.png/.jpg/.jpeg/.gif/.webp) return the IMAGE ITSELF as native MCP image content (plus a one-line text note naming the file), so you can look at the picture — up to 3.5 MB of raw image data; a larger image gets an honest refusal asking for a locally downscaled copy or a smaller export (`.svg` is text and reads as text). Images come back only on a DIRECT call: inside `call_tool_chain` an image read yields an `{ image_omitted, note }` stub instead. Office and OpenDocument files (.docx/.pptx/.xlsx, .odt/.odp/.ods) and PDFs return their EXTRACTED text under an honest `[extracted text of …]` header, with `[slide N]`/`[sheet: Name]`/`[page N]` markers — the extraction is READ-ONLY (layout/images omitted; such files cannot be edited as text, only replaced by uploading a new version). Email files (.eml/.msg) return their EXTRACTED text the same way: a `[from]`/`[to]`/`[subject]`/`[date]` header block, the body (plain-text part preferred; an HTML-only body is stripped to text), and an `[attachments]` name list — attachments are listed, never extracted. Other binary files return a one-line description instead of raw bytes. Optional `offset`/`limit` slice the content (characters for a file, bytes for a `__tool_chain_spill__/…` ref; ignored for an image) — use them to page through large files or a `call_tool_chain` spill rather than reading multi-MB in full. A spill ref is workspace-independent: `branch` is ignored for it.' +
-            ONTOLOGY_BOUNDARY_NOTE,
+        gated: true,
+        description: 'Read a workspace file as text. Returns `{ path, content }`. What comes back for a document, an email file, an image ' +
+            'or any other binary file is the content rule\'s business (see the shared rules): text files as text, documents and ' +
+            'email files as extracted text, an image as the picture itself, anything else as a one-line description. ' +
+            'Optional `offset`/`limit` slice the content (characters for a file, bytes for a `__tool_chain_spill__/…` ref; ignored ' +
+            'for an image) — use them to page through large files or a `call_tool_chain` spill rather than reading multi-MB in full. ' +
+            'It also reads a `__tool_chain_spill__/…` ref back from a truncated `call_tool_chain`: such a ref belongs to no ' +
+            'workspace, so `branch` is ignored for it.',
         inputs: {
             type: 'object',
             properties: {
@@ -1120,12 +1371,12 @@ changeGate) {
             if (spillStore.isSpillRef(p)) {
                 return { path: p, content: await spillStore.read(p, offset, limit) };
             }
-            await recordOntologyRead(sessionOntologyGate, ctx, p);
+            await notifyAgentRead(agentAccessGate, ctx, a.branch, p);
             await assertCanRead(readGateFor(a.branch, ctx), p);
             const fs = await ctx.getFilesystem(a.branch);
             // Reading (extraction, image and binary handling included) happens AFTER
-            // the access gate and the ontology-read recording above — a document
-            // read is still a KB read. ONE registry dispatch picks the reader by
+            // the access gate and the read hook above — a document read is still a
+            // KB read. ONE registry dispatch picks the reader by
             // extension; everything below just maps its ReadResult onto the tool's
             // result shape.
             const bytes = await orNotFound(p, async () => asBytes(await fs.readFile(p)));
@@ -1157,8 +1408,8 @@ changeGate) {
     });
     mount({
         name: 'list_files',
-        description: `List a directory. Returns \`{ path, entries: [{ name, type, size? }] }\`. Omit \`path\` for the workspace root, which holds the repository as the \`${kbDirName}/\` folder: every content path is under it (e.g. \`${kbDirName}/KnowledgeBase\`), and a path given without that prefix is placed under it.` +
-            ONTOLOGY_BOUNDARY_NOTE,
+        gated: true,
+        description: `List a directory. Returns \`{ path, entries: [{ name, type, size? }] }\`. Omit \`path\` for the workspace root, which holds the repository as the \`${kbDirName}/\` folder: every content path is under it (e.g. \`${kbDirName}/KnowledgeBase\`), and a path given without that prefix is placed under it.`,
         inputs: {
             type: 'object',
             properties: {
@@ -1188,7 +1439,7 @@ changeGate) {
         write: false,
         handler: async (a, ctx) => {
             const dir = a.path || '';
-            await recordOntologyRead(sessionOntologyGate, ctx, dir);
+            await notifyAgentRead(agentAccessGate, ctx, a.branch, dir);
             const fs = await ctx.getFilesystem(a.branch);
             const entries = withoutPlaceholder((await fs.readdir(dir || '.')));
             const filtered = await filterReadableEntries(readGateFor(a.branch, ctx), dir, entries);
@@ -1197,13 +1448,18 @@ changeGate) {
     });
     mount({
         name: 'file_stat',
-        description: () => 'Get a file/directory\'s metadata (name, type, size, …) without returning content. A file also reports `contentMode`: `text` (read, write and edit it as text), `document` (read returns an extraction; replace it by upload) or `binary` (bytes: copy, move, delete, or replace by upload), plus `kind` (`text` | `document` | `image` | `binary`), `mime`, `mimeSource` and `textEditable` — decided by the same file readers read_file, grep and the write tools use, so an extensionless text file is `text/plain`.' +
-            ' Every entry also reports what you may DO with it. ' +
-            `\`managed\` is true for a platform item — a platform file (${platformFileList(kb.layout)}) or a platform folder (the repository root or a reserved root folder such as \`KnowledgeBase/\`); managed items are never movable or deletable through these tools. ` +
-            '`access: { read, write, download, owner }` is your own verdict under the access rules; pass `explainAccess: true` to learn why, and who else holds each verb. `movable` and `deletable` say whether `move_file` / `delete_file` / `delete_folder` would be allowed for you, judged like their dry runs: not managed, no symbolic link, and on a protected branch you hold write on the item AND on every file under a folder (on a draft branch writes are not gated). `movable` judges the source side only; the destination is judged by a `move_file` dry run. ' +
-            'For a folder, `descendants` is the number of files under it at any depth; counting stops at 10000 and `descendantsTruncated` says so, and past that point `movable` and `deletable` are false because a folder that large was not judged in full — run the `move_file` or `delete_folder` dry run for the real verdict. ' +
-            'Call this before a move or delete to see what it would touch.' +
-            ONTOLOGY_BOUNDARY_NOTE,
+        gated: true,
+        description: 'Get a file/directory\'s metadata (name, type, size, …) without returning content, and what you may DO with it. ' +
+            'A file also reports `contentMode`, `kind`, `mime`, `mimeSource` and `textEditable` — decided by the same readers ' +
+            'read_file, grep and the write tools use, so an extensionless text file is `text/plain`. ' +
+            '`access: { read, write, download, owner }` is your own verdict under the access rules; pass `explainAccess: true` to ' +
+            'learn why, and who else holds each verb. ' +
+            'Call this before a move or delete: `managed`, `movable` and `deletable` answer the shared rules on what these tools ' +
+            'never move or delete, judged like the dry runs (on a draft branch writes are not gated); `movable` judges the SOURCE ' +
+            'side only, so the destination still wants a `move_file` dry run. ' +
+            'For a folder, `descendants` counts the files under it at any depth; counting stops at 10000 and ' +
+            '`descendantsTruncated` says so, past which `movable` and `deletable` are false — a folder that large was not judged ' +
+            'in full, so run the `move_file` or `delete_folder` dry run for the real verdict.',
         inputs: {
             type: 'object',
             properties: {
@@ -1276,7 +1532,7 @@ changeGate) {
         handler: async (a, ctx) => {
             const p = a.path;
             const branch = a.branch;
-            await recordOntologyRead(sessionOntologyGate, ctx, p);
+            await notifyAgentRead(agentAccessGate, ctx, branch, p);
             await assertCanRead(readGateFor(branch, ctx), p);
             // Nothing there is a 404, and the placeholder — never content — gets
             // exactly that answer: the one every file tool gives (see not-found.ts).
@@ -1378,8 +1634,8 @@ changeGate) {
     });
     mount({
         name: 'grep',
-        description: 'Regex content search across the workspace. Returns `{ matches: [{ path, line, text }] }` (capped). Use to find where something is defined/referenced. `path` may name a DIRECTORY (searches the subtree) or a single FILE (searches just that file); a path with nothing at it is an error, never an empty result. Searches INSIDE Office and OpenDocument files (.docx/.pptx/.xlsx, .odt/.odp/.ods), PDFs and email files (.eml/.msg) via their extracted text — matches there carry the extraction\'s line numbers, and the `[slide N]`/`[sheet: Name]`/`[page N]`/`[from]`/`[subject]` marker lines locate them; a bounded number of not-yet-extracted documents is extracted per call, and the result notes how many were skipped (re-run to cover them).' +
-            ONTOLOGY_BOUNDARY_NOTE,
+        gated: true,
+        description: 'Regex content search across the workspace. Returns `{ matches: [{ path, line, text }] }` (capped). Use to find where something is defined/referenced. `path` may name a DIRECTORY (searches the subtree) or a single FILE (searches just that file); a path with nothing at it is an error, never an empty result. Searches INSIDE Office and OpenDocument files (.docx/.pptx/.xlsx, .odt/.odp/.ods), PDFs and email files (.eml/.msg) via their extracted text — matches there carry the extraction\'s line numbers, and the `[slide N]`/`[sheet: Name]`/`[page N]`/`[from]`/`[subject]` marker lines locate them; a bounded number of not-yet-extracted documents is extracted per call, and the result notes how many were skipped (re-run to cover them).',
         inputs: {
             type: 'object',
             properties: {
@@ -1430,11 +1686,10 @@ changeGate) {
             // (an empty path is the handler's to explain), and here it would
             // otherwise name the workspace directory by another spelling.
             const searchRoot = typeof a.path === 'string' && a.path.length > 0 ? a.path : kbDirName;
-            // The search root itself is checked here (fail-closed for an agent grep on
-            // a named subtree with no sessionId); each file the walk actually opens is
-            // recorded per-file below, so a root-level grep that reaches into multiple
-            // ontologies still records each one (and can poison later writes).
-            await recordOntologyRead(sessionOntologyGate, ctx, searchRoot);
+            // The search root itself goes to the read hook here; each file the walk
+            // actually opens goes to it per-file below, so a hook sees every path a
+            // grep reached rather than only the root it started from.
+            await notifyAgentRead(agentAccessGate, ctx, a.branch, searchRoot);
             const fs = await ctx.getFilesystem(a.branch);
             const gate = readGateFor(a.branch, ctx);
             const out = [];
@@ -1452,7 +1707,7 @@ changeGate) {
             /** Why a single-file search found nothing, when "no matches" would be a lie. */
             let fileNote;
             if (kind === 'directory') {
-                await grepWalk(fs, searchRoot, re, out, max, 0, gate, (p) => recordOntologyRead(sessionOntologyGate, ctx, p), docs);
+                await grepWalk(fs, searchRoot, re, out, max, 0, gate, (p) => notifyAgentRead(agentAccessGate, ctx, a.branch, p), docs);
             }
             else {
                 // Not a directory: the permission verdict comes BEFORE every other
@@ -1491,11 +1746,10 @@ changeGate) {
     // ── writes (through the lock/commit pipeline) ───────────────────────────
     mount({
         name: 'write_file',
+        gated: true,
         description: 'Write a workspace TEXT file. The change is committed + pushed as you. Returns `{ path, bytes, outcome }`, where `outcome` is ' +
             '`created`, `replaced` or `updated`.' +
-            WRITE_MODE_NOTE +
-            IMAGE_CONVENTION_NOTE +
-            ONTOLOGY_BOUNDARY_NOTE,
+            UPLOAD_ROUTE_NOTE,
         inputs: {
             type: 'object',
             properties: {
@@ -1531,7 +1785,7 @@ changeGate) {
             // (today only `watchlist_check`, to `.html`). Unrestricted sessions pass straight
             // through (see `assertPathWritable`), so it does not limit other agents.
             writePolicy.assertPathWritable(ctx.sessionId, a.path);
-            await assertOntologyWriteAllowed(sessionOntologyGate, ctx, a.path);
+            await assertAgentWriteAllowed(agentAccessGate, ctx, a.branch, a.path);
             const mode = modeOf(a);
             const fs = await ctx.getFilesystem(a.branch);
             await assertNotBinaryOverwrite(readers, a.path, fs);
@@ -1564,17 +1818,16 @@ changeGate) {
     });
     mount({
         name: 'write_files',
+        gated: true,
         description: 'Batch-write many files in ONE commit — far faster than calling write_file once per file when ' +
             'creating many files at once (e.g. seeding a knowledge base). Each entry is `{ path, content }`, and the files it ' +
             'writes are committed + pushed together as you. Prefer this over many write_file ' +
-            'calls. All files must be in the SAME ontology (the boundary below applies to the batch). Text files only. ' +
+            'calls. Text files only. ' +
             'Returns `{ count, files }`: one entry per REQUESTED path, in the order you gave them, each `{ path, outcome }` — ' +
             '`created` / `replaced` / `updated` for a path it wrote, or `refused` with `error` (the code) and `message` (why) for a ' +
             'path it could not. `count` is how many were written. A path it refuses — the mode said no, or the file is not text — ' +
             'does not stop the others; read `files` to see what landed.' +
-            WRITE_MODE_NOTE +
-            IMAGE_CONVENTION_NOTE +
-            ONTOLOGY_BOUNDARY_NOTE,
+            UPLOAD_ROUTE_NOTE,
         inputs: {
             type: 'object',
             properties: {
@@ -1628,15 +1881,14 @@ changeGate) {
             if (files.length === 0)
                 return { count: 0, files: [] };
             const mode = modeOf(a);
-            // The POLICY gates still judge the whole batch: a restricted run or a
-            // cross-ontology batch is a call that should not have been made at all,
-            // not a per-path outcome, and the ontology gate must see every path
-            // before anything lands. What a single FILE is (not text) or what its
-            // path already holds (the mode) is decided per path, below.
+            // The POLICY gate still judges the whole batch: a restricted run is a
+            // call that should not have been made at all, not a per-path outcome.
+            // The write hook is asked PER PATH, below, so a path it refuses is that
+            // path's outcome and the rest of the batch still lands. What a single
+            // FILE is (not text) or what its path already holds (the mode) is
+            // decided per path too.
             for (const f of files)
                 writePolicy.assertPathWritable(ctx.sessionId, f.path);
-            for (const f of files)
-                await assertOntologyWriteAllowed(sessionOntologyGate, ctx, f.path);
             const fs = await ctx.getFilesystem(a.branch);
             // `write: true` guarantees a LockingFilesystem here; `writeFiles` lands the
             // batch as one commit. Structural cast avoids a workflow-internal import.
@@ -1657,6 +1909,19 @@ changeGate) {
             for (const f of files) {
                 const entry = { path: f.path };
                 outcomes.push(entry);
+                try {
+                    await assertAgentWriteAllowed(agentAccessGate, ctx, a.branch, f.path);
+                }
+                catch (err) {
+                    // A DELIBERATE refusal by the deployment's write hook is this path's
+                    // outcome and no more: its message is what the caller is meant to
+                    // read, and one refused path must not take the others down. Anything
+                    // else the hook throws is not a verdict — it is the gate itself
+                    // failing — so `refuse` rethrows it and the whole batch fails loudly,
+                    // exactly as it does in `write_file`.
+                    refuse(entry, err);
+                    continue;
+                }
                 try {
                     assertNotDocumentEdit(readers, f.path);
                     await assertNotBinaryOverwrite(readers, f.path, fs);
@@ -1724,8 +1989,9 @@ changeGate) {
     });
     mount({
         name: 'edit_file',
+        gated: true,
         description: 'Replace an exact string in a workspace TEXT file. `old_string` must appear exactly once unless `replace_all`. Committed + pushed as you.' +
-            ONTOLOGY_BOUNDARY_NOTE,
+            UPLOAD_ROUTE_NOTE,
         inputs: {
             type: 'object',
             properties: {
@@ -1749,7 +2015,7 @@ changeGate) {
         handler: async (a, ctx) => {
             assertNotDocumentEdit(readers, a.path);
             writePolicy.assertPathWritable(ctx.sessionId, a.path);
-            await assertOntologyWriteAllowed(sessionOntologyGate, ctx, a.path);
+            await assertAgentWriteAllowed(agentAccessGate, ctx, a.branch, a.path);
             const fs = await ctx.getFilesystem(a.branch);
             const path = a.path;
             const oldStr = a.old_string;
@@ -1773,9 +2039,8 @@ changeGate) {
     });
     mount({
         name: 'delete_file',
-        description: () => 'Delete ONE workspace file (a symbolic link is refused: links are never followed or removed). Committed + pushed as you. Its folder stays, even when this was its last file. Files only: a folder is refused with a pointer to `delete_folder`. ' +
-            `A platform file (\`access.md\` or \`.bevelignore\` in any folder, \`roles.yaml\` or \`${kb.layout.agentsFile}\` at the repository root) and git metadata are refused.` +
-            ONTOLOGY_BOUNDARY_NOTE,
+        gated: true,
+        description: 'Delete ONE workspace file. Committed + pushed as you. Its folder stays, even when this was its last file. Files only: a folder is refused with a pointer to `delete_folder`.',
         inputs: {
             type: 'object',
             properties: {
@@ -1794,14 +2059,14 @@ changeGate) {
         write: true,
         proposable: true,
         handler: async (a, ctx) => {
-            // A delete propagates no cross-ontology information (it removes a node, it
-            // doesn't carry bytes from elsewhere), so it is NOT ontology-write-gated — it
-            // only records the ontology it touched, like a read. The extension policy
-            // DOES apply though: a dashboard-only run must not delete graph `.md` nodes.
+            // A delete carries no bytes from anywhere else — it removes a node — so
+            // it goes to the READ hook, like a read, not the write hook. The
+            // extension policy DOES apply though: a dashboard-only run must not
+            // delete graph `.md` nodes.
             const path = a.path;
             const branch = a.branch;
             writePolicy.assertPathWritable(ctx.sessionId, path);
-            await recordOntologyRead(sessionOntologyGate, ctx, path);
+            await notifyAgentRead(agentAccessGate, ctx, branch, path);
             const fs = await ctx.getFilesystem(branch);
             assertPlainPath(path);
             const root = await workspaceRoot(branch, ctx);
@@ -1827,12 +2092,14 @@ changeGate) {
     });
     mount({
         name: 'delete_folder',
+        gated: true,
         description: 'Delete a workspace FOLDER and every file under it, at any depth; the whole folder lands as ONE committed + pushed change as you — all of it or none of it — then the empty folder is removed. This is the one way a folder goes away: the folder that held it stays, even if this was all it had, and a folder holding nothing but its empty-folder placeholder counts as empty. ' +
-            'Preflight first: `dryRun: true` changes nothing and answers `{ path, kind: "folder", descendants, files, filesTruncated, allowed, reason? }` — `descendants` is the file count, `files` names up to 100 of them. ' +
-            'A non-empty folder is deleted only with `confirm: true`; without it the call deletes nothing and returns the same impact with `confirmationRequired: true`. Do NOT set `confirm: true` on your first call — dry-run, check the impact, then confirm. ' +
-            'Refused (in a dry run as `allowed: false` with the `reason`): a platform folder (the repository root or a reserved root folder such as `KnowledgeBase/`), git metadata, a folder holding a symbolic link (links are never removed), and a folder holding any file you may not write. A path that is a file is refused with a pointer to `delete_file`, and a path through a symbolic link is refused (links are never followed). ' +
-            'The folder\'s own platform files (`access.md`, `.bevelignore`) go with it in that same one change, so its files are never left ungoverned part-way; you must be able to write those platform files too.' +
-            ONTOLOGY_BOUNDARY_NOTE,
+            'The dry run answers `{ path, kind: "folder", descendants, files, filesTruncated, allowed, reason? }` — `descendants` is ' +
+            'the file count, `files` names up to 100 of them — and a non-empty folder wants `confirm: true`. ' +
+            'Beyond what the shared rules refuse, a folder HOLDING a symbolic link, or any file you may not write, is refused ' +
+            '(the link itself is never removed), and a path that is a FILE ' +
+            'is refused with a pointer to `delete_file`. You must be able to write the folder\'s own platform files too: they go ' +
+            'with it in that same one change, so its files are never left ungoverned part-way.',
         inputs: {
             type: 'object',
             properties: {
@@ -1870,7 +2137,7 @@ changeGate) {
             // The normaliser has already placed the path inside the repository; this
             // is the check that it really is in there before a folder is walked.
             assertInsideRepo(path, kbDirName);
-            await recordOntologyRead(sessionOntologyGate, ctx, path);
+            await notifyAgentRead(agentAccessGate, ctx, branch, path);
             const fs = await ctx.getFilesystem(branch);
             const kind = await kindOf(fs, path);
             if (kind === null)
@@ -1964,7 +2231,8 @@ changeGate) {
     });
     mount({
         name: 'mkdir',
-        description: 'Create a directory (recursive). It lists as an empty folder and persists in git until it is deleted explicitly.' + ONTOLOGY_BOUNDARY_NOTE,
+        gated: true,
+        description: 'Create a directory (recursive). It lists as an empty folder and persists in git until it is deleted explicitly.',
         inputs: {
             type: 'object',
             properties: {
@@ -1984,18 +2252,22 @@ changeGate) {
         proposable: true,
         handler: async (a, ctx) => {
             writePolicy.assertPathWritable(ctx.sessionId, a.path);
-            await assertOntologyWriteAllowed(sessionOntologyGate, ctx, a.path);
+            await assertAgentWriteAllowed(agentAccessGate, ctx, a.branch, a.path);
             await (await ctx.getFilesystem(a.branch)).mkdir(a.path, { recursive: true });
             return { path: a.path, created: true };
         },
     });
     mount({
         name: 'move_file',
-        description: () => 'Move or rename a workspace FILE or FOLDER; a folder moves recursively, with everything under it. `dest` is the full new path, not the folder to move into. Lands as a delete + create, committed + pushed as you. ' +
-            `Rules: the destination must not exist — a move never overwrites a file or merges into a folder; a platform file (\`access.md\` or \`.bevelignore\` in any folder, \`roles.yaml\` or \`${kb.layout.agentsFile}\` at the repository root) is refused with "<name> is a platform file and stays in its folder." — a folder that moves takes its own platform files along, still in their folder; a platform folder (the repository root or a reserved root folder such as \`KnowledgeBase/\`) and git metadata are refused; a move cannot create a platform file or folder at \`dest\` either (renaming a note to \`access.md\` is refused); a path through a symbolic link is refused, since links are never followed; on a protected branch you must be able to write both ends — for a folder, every file under it at its old and its new path. ` +
-            'Access follows the destination folder. Preflight first: `dryRun: true` changes nothing and answers `{ src, dest, kind, descendants, access: { before, after }, accessChanges, allowed, reason? }` — `access` is your own `{ read, write, download, owner }` at the source and at the destination. ' +
-            'A move whose `accessChanges` is true runs only with `confirm: true`; without it the call moves nothing and returns the same impact with `confirmationRequired: true`. Do NOT set `confirm: true` on your first call — dry-run, check the impact, then confirm.' +
-            ONTOLOGY_BOUNDARY_NOTE,
+        gated: true,
+        // A plain string again: what refuses a move names the guide, and that is in
+        // the shared rules now, which are rebuilt from the layout where they live.
+        description: 'Move or rename a workspace FILE or FOLDER; a folder moves recursively, with everything under it. `dest` is the full new path, not the folder to move into. Lands as a delete + create, committed + pushed as you. ' +
+            'The destination must not exist — a move never overwrites a file or merges into a folder. Access follows the ' +
+            'DESTINATION folder, so a move can change what you (and others) may do with the file: the dry run answers ' +
+            '`{ src, dest, kind, descendants, access: { before, after }, accessChanges, allowed, reason? }`, where `access` is your ' +
+            'own `{ read, write, download, owner }` at the source and at the destination AS IT WILL BE once the move has landed, ' +
+            'with every `access.md` inside a moved folder counted at its new place, and a move whose `accessChanges` is true wants `confirm: true`.',
         inputs: {
             type: 'object',
             properties: {
@@ -2016,8 +2288,8 @@ changeGate) {
                 dest: str('Destination path (echoes the input).'),
                 kind: str('`file` or `folder`.'),
                 descendants: int('Files that move: 1 for a file, the file count under a folder.'),
-                access: { type: 'object', description: 'Your `{ read, write, download, owner }` at the source (`before`) and destination (`after`).' },
-                accessChanges: { type: 'boolean', description: 'True when any of your verdicts differs between source and destination.' },
+                access: { type: 'object', description: 'Your `{ read, write, download, owner }` at the source (`before`) and at the destination once the move has landed (`after`).' },
+                accessChanges: { type: 'boolean', description: 'True when any of your verdicts differs between `before` and `after`.' },
                 allowed: { type: 'boolean', description: 'Whether the move may run.' },
                 reason: str('Why it may not, when `allowed` is false.'),
                 dryRun: { type: 'boolean', description: 'True on a dry run.' },
@@ -2035,12 +2307,12 @@ changeGate) {
             const src = a.src.replace(/\/+$/, '');
             const dest = a.dest.replace(/\/+$/, '');
             const branch = a.branch;
-            // A move CARRIES the source content into the destination — a genuine
-            // cross-ontology flow if the two differ — so BOTH endpoints are write-gated
-            // (unlike a plain delete, which moves no content). Check both BEFORE
-            // touching disk so a blocked endpoint can't leave the source already deleted.
-            await assertOntologyWriteAllowed(sessionOntologyGate, ctx, src);
-            await assertOntologyWriteAllowed(sessionOntologyGate, ctx, dest);
+            // A move CARRIES the source content into the destination, so BOTH ends
+            // go to the write hook (unlike a plain delete, which moves no content).
+            // Ask about both BEFORE touching disk, so a refused end can't leave the
+            // source already deleted.
+            await assertAgentWriteAllowed(agentAccessGate, ctx, branch, src);
+            await assertAgentWriteAllowed(agentAccessGate, ctx, branch, dest);
             const fs = await ctx.getFilesystem(branch);
             const root = await workspaceRoot(branch, ctx);
             // Before the kind check, which stats THROUGH a link: a dangling link at
@@ -2057,8 +2329,13 @@ changeGate) {
                 writePolicy.assertPathWritable(ctx.sessionId, f);
                 writePolicy.assertPathWritable(ctx.sessionId, dest + f.slice(src.length));
             }
-            const [before, after] = await Promise.all([accessAt(branch, ctx, src), accessAt(branch, ctx, dest)]);
-            const accessChanges = Object.keys(before).some((v) => before[v] !== after[v]);
+            // `after` is the destination as it WILL be — with the `access.md` files
+            // under `src` counted where they land. See `accessAfter`.
+            const [before, after] = await Promise.all([
+                accessAt(branch, ctx, src),
+                accessAfter(branch, ctx, src, dest),
+            ]);
+            const accessChanges = verbsDiffer(before, after);
             // The placeholder moves with its folder, but it is never content.
             const descendants = srcFiles.filter((f) => !isFolderPlaceholder(f)).length;
             // Neither end may be the platform's own: a move neither takes a platform
@@ -2153,14 +2430,17 @@ changeGate) {
     });
     mount({
         name: 'copy_file',
-        description: 'Copy a workspace file to a new path. The destination must not exist — like a move, a copy never overwrites a file or a folder; to change what is in a file that already exists, write it. Committed + pushed as you.'
-            + ONTOLOGY_BOUNDARY_NOTE,
+        gated: true,
+        description: 'Copy a workspace FILE to a new path. The destination must not exist — like a move, a copy never overwrites a file or a folder; to change what is in a file that already exists, write it. Committed + pushed as you. ' +
+            'Preflight first: `dryRun: true` changes nothing and answers `{ src, dest, kind, descendants, access: { before, after }, accessChanges, allowed, reason? }` — `access` is your own `{ read, write, download, owner }` at the source and at the destination AS IT WILL BE once the copy has landed, with every `access.md` inside a copied folder counted at its new place. ' +
+            'One exception to that shape: when the destination is one you may not write, the answer is the refusal alone — `allowed: false` with `reason`, and no `kind` and no `descendants`, because nothing about the source is read before that verdict.',
         inputs: {
             type: 'object',
             properties: {
                 branch: BRANCH_INPUT,
                 src: wsPath(kbDirName, 'Source path'),
                 dest: wsPath(kbDirName, 'Destination path — must not exist yet'),
+                dryRun: { type: 'boolean', description: 'Answer with the impact and change nothing.' },
                 sessionId: SESSION_ID_INPUT,
             },
             required: ['branch', 'src', 'dest'],
@@ -2168,20 +2448,30 @@ changeGate) {
         },
         outputs: {
             type: 'object',
-            properties: { src: str('Source path (echoes the input).'), dest: str('Destination path (echoes the input).'), copied: { type: 'boolean', description: 'Always true on success.' } },
+            properties: {
+                src: str('Source path (echoes the input).'),
+                dest: str('Destination path (echoes the input).'),
+                kind: str('`file` or `folder` (dry run only; absent when `allowed` is false because you may not write the destination).'),
+                descendants: int('Files the copy would carry: 1 for a file, the file count under a folder (dry run only; absent when `allowed` is false because you may not write the destination).'),
+                access: { type: 'object', description: 'Your `{ read, write, download, owner }` at the source (`before`) and at the destination once the copy has landed (`after`) — dry run only.' },
+                accessChanges: { type: 'boolean', description: 'True when any of your verdicts differs between `before` and `after` (dry run only).' },
+                allowed: { type: 'boolean', description: 'Whether the copy may run (dry run only).' },
+                reason: str('Why it may not, when `allowed` is false.'),
+                dryRun: { type: 'boolean', description: 'True on a dry run.' },
+                copied: { type: 'boolean', description: 'True once the copy landed; false on a dry run.' },
+            },
             required: ['src', 'dest', 'copied'],
         },
         write: true,
         proposable: true,
         handler: async (a, ctx) => {
-            // A copy CARRIES the source content into the destination — a genuine
-            // cross-ontology flow if the two differ — so BOTH endpoints are write-gated.
-            // Check both before touching disk.
+            // A copy CARRIES the source content into the destination, so BOTH ends
+            // go to the write hook. Ask about both before touching disk.
             writePolicy.assertPathWritable(ctx.sessionId, a.src);
             writePolicy.assertPathWritable(ctx.sessionId, a.dest);
-            await assertOntologyWriteAllowed(sessionOntologyGate, ctx, a.src);
-            await assertOntologyWriteAllowed(sessionOntologyGate, ctx, a.dest);
             const branch = a.branch;
+            await assertAgentWriteAllowed(agentAccessGate, ctx, branch, a.src);
+            await assertAgentWriteAllowed(agentAccessGate, ctx, branch, a.dest);
             const src = a.src;
             const dest = a.dest;
             // A copy lands bytes at a name of its own, so it is refused by the same
@@ -2193,6 +2483,8 @@ changeGate) {
             // own containment check: a path with a `..` segment must not reach
             // `lstat` outside the workspace, even to be told a name is taken.
             assertPlainPath(dest);
+            if (a.dryRun === true)
+                return copyImpact(branch, ctx, src, dest);
             // The write verdict comes FIRST, for the reason `move_file` gives at
             // length: "already exists" is a fact about the destination folder, and a
             // caller who may not write there must not be told it. The lock gate
@@ -2232,6 +2524,12 @@ changeGate) {
                 await asEntryExists(() => fs.copyFile(src, dest));
             }
             catch (err) {
+                // The filesystem's own "that is a directory" becomes the sentence the
+                // dry run predicts, instead of escaping as a 500 carrying the
+                // server's absolute path.
+                if (err?.name === 'IsDirectoryError') {
+                    throw new ToolError(folderCopyRefusal(src), 400);
+                }
                 const missing = isAbsence(err) || err.name === 'FileNotFoundError';
                 if (missing) {
                     throw (await kindOf(fs, src)) === null
@@ -2245,8 +2543,8 @@ changeGate) {
     });
     mount({
         name: 'unzip',
-        description: 'Extract a .zip already in the workspace (defaults to the zip\'s parent). Returns extracted files + skipped entries. Existing files are overwritten.' +
-            ONTOLOGY_BOUNDARY_NOTE,
+        gated: true,
+        description: 'Extract a .zip already in the workspace (defaults to the zip\'s parent). Returns extracted files + skipped entries. Existing files are overwritten.',
         inputs: {
             type: 'object',
             properties: {
@@ -2278,19 +2576,19 @@ changeGate) {
         write: true,
         handler: async (a, ctx) => {
             const zipPath = a.path;
-            // Reading the source archive pins/records the source ontology, so a session
-            // can't unzip from ontology A into ontology B without the A read counting.
-            await recordOntologyRead(sessionOntologyGate, ctx, zipPath);
+            // Opening the archive is a read of the archive, so the read hook hears
+            // about it before a single entry is extracted out of it.
+            await notifyAgentRead(agentAccessGate, ctx, a.branch, zipPath);
             // A .zip that is not there is a missing PATH, not an unreadable archive:
             // the service now says so (PathNotFoundError) and the helper turns it
             // into the same 404 every other file tool answers. Only that declared
             // answer maps — a failure part-way through an extraction is not the
             // archive going missing.
             return orDeclaredNotFound(() => ctx.workspaceService.unzipFile(workspaceIdForBranch(a.branch), zipPath, typeof a.destination === 'string' ? a.destination : undefined, 
-            // Each extracted file is a write: a cross-ontology or write-blocked entry
-            // is skipped (not extracted), so an archive can't bypass the boundary — the
-            // extension policy applies per entry too, so a restricted run can't unzip a
-            // `.md` into the graph.
+            // Each extracted file is a write of its own: an entry the write
+            // hook refuses is skipped (not extracted), so an archive can't be
+            // a way around it — the extension policy applies per entry too, so
+            // a restricted run can't unzip a `.md` into the graph.
             (wsRelPath) => {
                 // An entry that would land beside the repository is skipped with the
                 // corrected-path reason, like any other refused entry.
@@ -2301,15 +2599,309 @@ changeGate) {
                     throw new ToolError('roles.yaml is never extracted from an archive — change it with edit_file or write_file, where the change is checked.', 422);
                 }
                 writePolicy.assertPathWritable(ctx.sessionId, wsRelPath);
-                return assertOntologyWriteAllowed(sessionOntologyGate, ctx, wsRelPath);
+                return assertAgentWriteAllowed(agentAccessGate, ctx, a.branch, wsRelPath);
             }), 'Nothing to extract');
         },
     });
+    // ── uploads (bytes that never pass through the model) ───────────────────
+    //
+    // The pair exists because MCP tool arguments are JSON. Every byte an agent
+    // sends through `write_file` is first typed out by the model, which
+    // truncates long files, mangles backslash and `\u` escapes, and cannot carry
+    // a PNG at all. `request_file_upload` answers an address; the agent POSTs
+    // the file (or one zip holding many) there with any HTTP client;
+    // `apply_file_upload` lands it on a branch in one commit. The bytes go from
+    // the agent's disk to the server's and never enter a prompt.
+    //
+    /**
+     * Why one of an upload's paths may not be landed, judged on the path ALONE —
+     * or undefined when nothing about the name itself refuses it.
+     *
+     * The platform files are the whole of it. `access.md` governs who may read
+     * and write the folder it sits in, `roles.yaml` says which roles exist, and
+     * the agent guide is read as instructions: each is configuration the platform
+     * obeys, and each has a write path that CHECKS the change (the roles gate
+     * refuses an edit that would lock every admin out; a folder's access rules
+     * are judged against who is asking). Bytes arriving by upload meet none of
+     * those gates — they are a buffer the sender chose — so an upload never
+     * lands one, whatever else the caller may write. `unzip` has refused
+     * `roles.yaml` from an archive for the same reason; this is that rule, over
+     * all four names.
+     */
+    const platformFileReason = (wsPath) => {
+        const rel = toKbRelative(wsPath, kbDirName);
+        return rel !== null && isPlatformFile(rel, kb.layout) ? platformFileUploadRefusal(rel) : undefined;
+    };
+    /**
+     * `apply_file_upload`'s handler: resolve the stored bytes into one path per
+     * file, judge each path the way `write_files` judges its own, and land the
+     * survivors as ONE commit.
+     *
+     * The judging is deliberately the same shape as `write_files`, down to the
+     * second verdict under the lock, because the promise the ticket makes is
+     * that an upload is judged "exactly as `write_file` would judge it". Three
+     * gates run per path and a path that fails one is that path's outcome and no
+     * more: the deployment's write hook, the platform-file rule above, and the
+     * `mode`. What is judged ONCE for the whole call is the destination — a
+     * caller who may not write the folder at all gets one refusal naming the
+     * change-request route, rather than the same refusal repeated per entry.
+     */
+    const applyFileUpload = async (a, ctx, uploads) => {
+        const branch = a.branch;
+        const token = a.token;
+        if (typeof token !== 'string' || token === '') {
+            throw new ToolError('Name the `token` `request_file_upload` answered with, after POSTing the file to its `uploadUrl`.', 400, { code: 'token-required' });
+        }
+        const mode = modeOf(a);
+        const destination = a.destination.replace(/\/+$/, '');
+        assertInsideRepo(destination, kbDirName);
+        // CLAIMED, not consumed: an apply refused whole (a protected destination,
+        // an archive that will not open) leaves the token alive so the caller can
+        // retry somewhere else rather than send the bytes again. The claim is what
+        // keeps it single-use meanwhile — a second apply finds the token in use.
+        const upload = uploads.claim(token, ctx.user.id);
+        let spent = false;
+        try {
+            const fs = await ctx.getFilesystem(branch);
+            const root = await workspaceRoot(branch, ctx);
+            // The destination, once, for the whole call. On a protected branch a
+            // caller who may not write the folder gets the lock gate's own refusal —
+            // which `rethrowAsWriteDenial` turns into `write-denied` with the
+            // change-request steps — and nothing lands.
+            const blockedDest = await writeBlocked(branch, ctx, [destination]);
+            if (blockedDest.length > 0)
+                throw await writeRefusal(branch, blockedDest[0], 'dir');
+            if ((await kindOf(fs, destination)) === 'file') {
+                throw new ToolError(`"${displayPath(destination)}" is a file, not a folder — \`destination\` names the folder the upload lands in.`, 409, { code: 'not_a_folder' });
+            }
+            const planned = await planUpload(upload, destination, kbDirName);
+            const paths = planned.filter((p) => p.content !== undefined).map((p) => p.path);
+            // One batched access read for every path, like `write_files` — empty on
+            // a draft branch, where changes reach a protected branch only through a
+            // change request.
+            const blocked = new Set(await writeBlocked(branch, ctx, paths));
+            const writes = [];
+            const outcomes = [];
+            /** The `files` entry for `writes[i]`, so the under-lock verdict can revise it. */
+            const entryOf = [];
+            for (const item of planned) {
+                const entry = { path: item.path };
+                outcomes.push(entry);
+                if (item.content === undefined) {
+                    entry.outcome = 'refused';
+                    entry.error = item.error;
+                    entry.message = item.message;
+                    continue;
+                }
+                const wsPathOf = item.path;
+                try {
+                    if (blocked.has(wsPathOf))
+                        throw await writeRefusal(branch, wsPathOf);
+                    const platform = platformFileReason(wsPathOf);
+                    if (platform !== undefined)
+                        throw new ToolError(platform, 422, { code: 'platform_file' });
+                    // The git folder is never a workspace path, in any spelling. A ZIP
+                    // entry's name has already met this rule in `zipEntryNameRefusal`; a
+                    // SINGLE uploaded file's has not — `.git` is a name the upload
+                    // route's `validateFilename` accepts — and the preflight that reads
+                    // the caller's own arguments never sees it either, because the name
+                    // came from the upload, not from the call. Asked here so that path
+                    // is REFUSED like any other, with the rest of the upload landing,
+                    // rather than failing the whole apply from inside `writeFiles`.
+                    assertNoGitInternalsSegment(wsPathOf);
+                    assertRepoRootNameFree(wsPathOf, kbDirName);
+                    // A link already on disk under the destination must not redirect
+                    // these bytes — the rule `unzip` applies per entry, applied here on
+                    // the path the write will take.
+                    const link = await symlinkOnPath(root, wsPathOf);
+                    if (link !== undefined) {
+                        throw new ToolError(`"${wsPathOf}" goes through the symbolic link "${link}"; an upload never follows links.`, 400, { code: 'symlink' });
+                    }
+                    writePolicy.assertPathWritable(ctx.sessionId, wsPathOf);
+                    await assertAgentWriteAllowed(agentAccessGate, ctx, branch, wsPathOf);
+                    // An earlier entry of this same upload counts as existing, as it
+                    // does in `write_files`: two `create` entries for one path are a
+                    // mistake the commit would otherwise hide.
+                    const exists = writes.some((w) => w.path === wsPathOf) || (await kindOf(fs, wsPathOf)) !== null;
+                    entry.outcome = decideWrite(mode, wsPathOf, exists);
+                    writes.push({ path: wsPathOf, content: item.content });
+                    entryOf.push(entry);
+                }
+                catch (err) {
+                    refuseEntry(entry, err);
+                }
+            }
+            // The mode gate again, with every path's lock held — the verdict the
+            // answer carries, for the reason `write_file` states at length. A path
+            // whose verdict changed under the lock is dropped from the batch and
+            // reported refused, leaving the rest to land.
+            const recheck = async (pending) => {
+                const kept = [];
+                for (let i = 0; i < pending.length; i++) {
+                    const entry = entryOf[i];
+                    try {
+                        const exists = kept.some((k) => k.path === pending[i].path) || (await kindOf(fs, pending[i].path)) !== null;
+                        entry.outcome = decideWrite(mode, pending[i].path, exists);
+                        kept.push(pending[i]);
+                    }
+                    catch (err) {
+                        refuseEntry(entry, err);
+                    }
+                }
+                return kept;
+            };
+            if (writes.length > 0) {
+                // `write: true` guarantees a LockingFilesystem here; `writeFiles` lands
+                // the whole set as ONE commit and takes a Buffer as content, so bytes
+                // reach disk exactly as they were sent — no text decode anywhere on
+                // the way, which is what makes a PNG and a backslash-heavy page land
+                // with the checksum they were uploaded with.
+                const batching = fs;
+                // In the DESTINATION folder's TURN, which `delete_folder` takes over the
+                // same subtree (and `keepFolderOf` with it). `writeFiles` creates the
+                // destination, and any folder above a zip entry on the way to it, as
+                // part of landing the batch — and a folder delete running between that
+                // creation and the commit enumerates the folder's files BEFORE these
+                // exist and then removes the folder they are landing in, which is an
+                // answer saying `created` for bytes that are already gone. The turn is
+                // taken OUTSIDE `writeFiles`, so it is held across the under-lock
+                // recheck and the commit both, and in the same order the delete takes
+                // its own (the folder's turn first, then each path's lock), which is
+                // what keeps two callers from waiting on each other's half.
+                await ctx.workspaceService.withFolderTurn(workspaceIdForBranch(branch), destination, async () => {
+                    await batching.writeFiles(writes, `Apply upload of ${writes.length} file(s)`, [], recheck);
+                });
+            }
+            // The token is spent once an ANSWER exists, even an answer in which
+            // every path was refused: the apply ran and said what happened at each
+            // path, and re-running it would say the same. Only a refusal that landed
+            // nothing AND answered nothing (thrown above) gives the token back.
+            spent = true;
+            await uploads.consume(token);
+            const listed = a.all === true ? outcomes : outcomes.slice(0, APPLY_ANSWER_CAP);
+            return {
+                destination,
+                count: outcomes.filter((o) => o.outcome !== 'refused').length,
+                total: outcomes.length,
+                files: listed,
+                ...(listed.length < outcomes.length ? { truncated: true } : {}),
+            };
+        }
+        finally {
+            if (!spent)
+                uploads.release(token);
+        }
+    };
+    // Mounted only when the composition supplied a store — see the `uploads`
+    // parameter. Core always does.
+    if (uploads) {
+        mount({
+            name: 'request_file_upload',
+            fileTool: false,
+            description: 
+            // Within the description cap (`tool-registry/description-length.ts`):
+            // why a file goes this way is one of the shared rules, and the header
+            // spelling of the token is on the `uploadUrl` output, where the
+            // address it changes is.
+            'Ask for a one-time address to send FILE BYTES to, so their content never passes through this conversation. ' +
+                'Use it for anything `write_file` cannot carry faithfully: a large file, a file full of backslashes or `\\u` ' +
+                'escapes, a binary file (a PNG, a PDF, a zip), or many files at once (zip them). ' +
+                'Returns `{ uploadUrl, token, expiresAt, expiresInSeconds, maxBytes }`. THEN: ' +
+                '(1) POST the file as the raw request body to `uploadUrl` with `?filename=<name>` — ' +
+                '`curl -X POST --data-binary @skill.zip "<uploadUrl>?filename=skill.zip"` — which answers what it received; ' +
+                '(2) call `apply_file_upload` with the same `token`, a `branch` and a destination folder. ' +
+                'One token carries one file or one zip, is bound to you and expires at `expiresAt`: an upload nobody applies ' +
+                'by then is deleted, and one over `maxBytes` is refused when you send it, naming the limit.',
+            inputs: { type: 'object', properties: {}, additionalProperties: false },
+            outputs: {
+                type: 'object',
+                properties: {
+                    uploadUrl: str('The absolute URL to POST the bytes to. Carries the token; add `?filename=<name>`. To keep the token out ' +
+                        'of a URL — when the command line you send from is logged or shared — POST to this address without its ' +
+                        'last (token) segment and send the token in an `x-upload-token` header instead.'),
+                    token: str('The token itself — what `apply_file_upload` takes, and what an `x-upload-token` header carries when you ' +
+                        'would rather it not sit in a URL. Treat it as a credential.'),
+                    expiresAt: str('ISO-8601 instant after which the token, and any bytes sent with it, are gone.'),
+                    expiresInSeconds: int('Seconds from now until `expiresAt`.'),
+                    maxBytes: int('The largest upload this deployment accepts, in bytes.'),
+                },
+                required: ['uploadUrl', 'token', 'expiresAt', 'expiresInSeconds', 'maxBytes'],
+            },
+            // A read-scoped caller has nothing to do with an upload token: the only
+            // thing it unlocks is a write. Refused at the handler factory, by scope,
+            // before the token is minted.
+            write: true,
+            handler: async (_a, ctx) => uploads.issue(ctx.user),
+        });
+        mount({
+            name: 'apply_file_upload',
+            gated: true,
+            description: 'Land a file you have already uploaded (see `request_file_upload`) in a folder on a branch, in ONE commit, as you. ' +
+                'A single file lands under the name it was sent with; a zip lands as its entries, keeping their folder structure. ' +
+                'Returns `{ destination, count, total, files }`: one entry per path, each `{ path, outcome }` — `created` / ' +
+                '`replaced` / `updated`, or `refused` with `error` (the code) and `message` (why). `count` is how many landed and ' +
+                '`total` how many paths there were; `files` is cut to the first 25 unless you pass `all: true`. ' +
+                'Every path is judged one by one — by your write access, the platform-file rules and what is already there — ' +
+                'exactly as `write_file` judges it, and a refused path does not stop the others. ' +
+                'The token is single-use: it is spent by the apply that lands it, and refused if you use it twice, let it ' +
+                'expire, or present one issued to somebody else. `mode` means what it means on `write_file`.',
+            inputs: {
+                type: 'object',
+                properties: {
+                    branch: BRANCH_INPUT,
+                    token: str('The `token` from `request_file_upload`, after you have POSTed the file to its `uploadUrl`.'),
+                    destination: wsPath(kbDirName, 'Folder the upload lands in (created if it is not there yet)'),
+                    mode: WRITE_MODE_INPUT,
+                    all: {
+                        type: 'boolean',
+                        description: 'List EVERY path in `files` instead of the first 25. `total` always says how many there were, so ask for ' +
+                            'all only when you need to read each outcome.',
+                    },
+                    sessionId: SESSION_ID_INPUT,
+                },
+                required: ['branch', 'token', 'destination'],
+                additionalProperties: false,
+            },
+            outputs: {
+                type: 'object',
+                properties: {
+                    destination: str('The folder the upload was applied to (echoes the input).'),
+                    count: int('How many paths landed — the entries in `files` whose `outcome` is not `refused`.'),
+                    total: int('How many paths the upload held, whether or not `files` lists them all.'),
+                    files: {
+                        type: 'array',
+                        description: 'One entry per path, in the order the upload held them. Cut to 25 unless `all` was true.',
+                        items: {
+                            type: 'object',
+                            properties: {
+                                path: str('The workspace path this entry was judged at.'),
+                                outcome: {
+                                    type: 'string',
+                                    enum: ['created', 'replaced', 'updated', 'refused'],
+                                    description: 'What happened at this path. `refused` means nothing was written there.',
+                                },
+                                error: str('Present when `outcome` is `refused`: the refusal code — e.g. `exists`, `missing`, `invalid_entry`, `platform_file`, `write-denied`.'),
+                                message: str('Present when `outcome` is `refused`: the full refusal, the same one `write_file` would have given.'),
+                            },
+                            required: ['path', 'outcome'],
+                        },
+                    },
+                    truncated: { type: 'boolean', description: 'True when `files` was cut: `total` is larger than what it lists. Pass `all: true` for the rest.' },
+                },
+                required: ['destination', 'count', 'total', 'files'],
+            },
+            write: true,
+            // So a protected-branch refusal arrives as `write-denied`, with the
+            // change-request steps, exactly as it does from write_file.
+            proposable: true,
+            handler: async (a, ctx) => applyFileUpload(a, ctx, uploads),
+        });
+    }
     // ── shell (internal-only) ───────────────────────────────────────────────
     mount({
         name: 'execute_command',
-        description: 'Run a shell command in the workspace directory. Returns `{ stdout, stderr, exitCode }` (output capped). Use for git status/log, grep/rg, build/test commands.' +
-            ONTOLOGY_BOUNDARY_NOTE,
+        gated: true,
+        description: 'Run a shell command in the workspace directory. Returns `{ stdout, stderr, exitCode }` (output capped). Use for git status/log, grep/rg, build/test commands.',
         internalOnly: true,
         fileTool: false,
         // The one tool the mount's branch check skips: the handler below resolves an
@@ -2397,11 +2989,12 @@ changeGate) {
                 throw new ToolError(`execute_command got an invalid \`branch\`: ${err.message} — ` +
                     'pass the exact branch (draft) whose workspace to run the command in.', 400);
             }
-            // Shell is a write path with no single target path to check, so enforce the
-            // boundary at the session level: refuse once the run is already write-blocked,
-            // or when the run is restricted to a file type (shell could write anything).
+            // Shell is a write path with no single target path to check, so the
+            // write hook is asked once for the call itself, with no path — and the
+            // run must not be restricted to a file type either, since shell could
+            // write anything.
             writePolicy.assertUnrestricted(ctx.sessionId);
-            await assertShellAllowedWithinOntology(sessionOntologyGate, ctx);
+            await assertAgentWriteAllowed(agentAccessGate, ctx, branch);
             // Canonical per-branch bootstrap entry point — it owns the workspace-id
             // encoding and the single-flight clone, so the shell never derives a
             // workspace path by hand.