feat(sim): F4.6f1 what a run leaves goes back into the document

The oracle SaveAfterRunRun saves Java's project after a run. The room writes
what a run leaves that Java keeps - files, running servers, virtual hosts,
mail servers' domains and accounts, mail programs' accounts and folders,
firewalls, DHCP clients' addresses - into the document as origin 'sim', at
most once a second, after each action and at the stop; writeRunState writes
only what differs. The command line now goes on in a folder made before a
restart, as Java's does.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>

packages/core/src/model/virtualFileSystem.ts

@@ -213,11 +213,17 @@ export function fileContentOfJavaType(rawType: string, content: string, path: st
 
 export class VirtualFileSystem {
   private store: Store;
+  private revisionValue = 0;
 
   constructor() {
     this.store = new Map([[keyOf('/'), { path: '/', content: { kind: 'directory' } }]]);
   }
 
+  /** Counts the changes: different after each one (the simulation room writes a file system back when it changed). */
+  get revision(): number {
+    return this.revisionValue;
+  }
+
   /** `init(entries:)`: shallow entries first; each parent must exist. */
   static fromEntries(entries: readonly VirtualFileEntry[]): VirtualFileSystem {
     const fileSystem = new VirtualFileSystem();
@@ -460,10 +466,12 @@ export class VirtualFileSystem {
     const key = keyOf(path);
     const existing = this.store.get(key);
     this.store.set(key, { path: existing?.path ?? path, content });
+    this.revisionValue += 1;
   }
 
   private delete(path: string): void {
     this.store.delete(keyOf(path));
+    this.revisionValue += 1;
   }
 
   private transaction(change: (candidate: VirtualFileSystem) => void): void {
@@ -471,6 +479,7 @@ export class VirtualFileSystem {
     change(candidate);
     candidate.validateQuotas();
     this.store = candidate.store;
+    this.revisionValue += 1;
   }
 
   private persistedEntryCount(): number {
@@ -538,6 +547,7 @@ export class VirtualFileSystem {
     candidate.set(destination, content);
     candidate.validateQuotas();
     this.store = candidate.store;
+    this.revisionValue += 1;
   }
 
   /** The subtree at `sourcePath`, shallow first. */