[Bug]: Cursor - failing until project hooks run

### Description

Workstation: MacBook Pro, Apple M3 Pro, macOS Tahoe 26.6.2
Cusor IDE: 3.18.9

Cursor IDE install step: Downloaded/installed from https://cursor.com/download

AI-DLC v2 install steps:
cd /tmp
git clone https://github.com/awslabs/aidlc-workflows.git
cd aidlc-workflows
git checkout v2
curl https://cursor.com/install -fsS | bash
bun dist/cursor/install.ts /Users/johnwhite/Documents/CursorProjects/transcript2
cd /Users/johnwhite/Documents/CursorProjects/transcript2
bun .cursor/tools/aidlc-utility.ts doctor
(confirmed all steps passed)

Steps to reproduce:
1. Load Cursor IDE (logged in via Pro subscription)
2. Opened up project folder: Users/johnwhite/Documents/CursorProjects/transcript2
3. Gave the following initial Intent: "/aidlc build me a super simple and minimalistic python application that accepts a single large transcript file and produces a losslessly cleaned transcript. The transcript lasts about 4 hours."

It goes through the first clarifying questions at aidlc/spaces/default/intents/260830-transcript-cleaner/inception/requirements-analysis/requirements-analysis-questions.md and I answer the questions within the file and save the file, and I choose "2. I'll edit the file — I'll fill in the answers in the file directly"

And I receive following error: "I can’t record that you’ll fill in the questions file yourself, because this session isn’t registering your replies. Presence checks will keep failing until Cursor’s project hooks actually run. Fully restart Cursor, then reopen this project and send /aidlc (or say you’re ready). After that, you can edit aidlc/spaces/default/intents/260830-transcript-cleaner/inception/requirements-analysis/requirements-analysis-questions.md and tell me done when the answers are in."

I restarted cursor and invoke again with "/aidlc continue where you left off, I choose 2. I'll edit the file — I'll fill in the answers in the file directly"

I then receive following error: "I can’t lock in Looks correct because Cursor still isn’t running this project’s hooks, so your reply isn’t counted as present for that confirmation. I have not written the requirements yet. Fully quit and restart Cursor, reopen this project, then send Looks correct (or /aidlc) again. After that confirmation records, I’ll generate the requirements."

### Steps to Reproduce

Steps to reproduce:
1. Load Cursor IDE (logged in via Pro subscription)
2. Opened up project folder: Users/johnwhite/Documents/CursorProjects/transcript2
3. Gave the following initial Intent: "/aidlc build me a super simple and minimalistic python application that accepts a single large transcript file and produces a losslessly cleaned transcript. The transcript lasts about 4 hours."

### Expected Behavior

Should not get errors, should continue like normal process.

### Actual Behavior

And I receive following error: "I can’t record that you’ll fill in the questions file yourself, because this session isn’t registering your replies. Presence checks will keep failing until Cursor’s project hooks actually run. Fully restart Cursor, then reopen this project and send /aidlc (or say you’re ready). After that, you can edit aidlc/spaces/default/intents/260830-transcript-cleaner/inception/requirements-analysis/requirements-analysis-questions.md and tell me done when the answers are in."

I restarted cursor and invoke again with "/aidlc continue where you left off, I choose 2. I'll edit the file — I'll fill in the answers in the file directly"

I then receive following error: "I can’t lock in Looks correct because Cursor still isn’t running this project’s hooks, so your reply isn’t counted as present for that confirmation. I have not written the requirements yet. Fully quit and restart Cursor, reopen this project, then send Looks correct (or /aidlc) again. After that confirmation records, I’ll generate the requirements."

### AI-DLC Version

v2 (current)

### Release / Commit

_No response_

### AI-DLC Phase

Inception (requirements, user stories, application design)

### Platform / IDE

Cursor IDE

### AI Model

Using Agent, Model Cursor Grok 4.6, High

### Environment

Workstation: MacBook Pro, Apple M3 Pro, macOS Tahoe 26.6.2
Cusor IDE: 3.18.9

### Additional Context

_No response_

Start with .cursor/tools/aidlc-utility.ts and the project-hook setup used by the v2 install, then reproduce the flow in Cursor through the requirements-analysis-questions.md file. Check why the user's edited answers and confirmation are not registered despite doctor passing. Done means the Inception flow records the response and continues without requiring repeated restarts.

Written by the indexing model from the issue text.