restore: recover all files wiped by empty-tree commit

[Copilot]

Commit 841c8e24 ("fix(setup): add AI token health check...") accidentally introduced an empty git tree (4b825dc6), deleting all 1681 repository files and causing every GitHub Actions workflow to fail with no source to execute.

Changes

• Restored full working tree from parent commit 8e5c573d — all 1681 files re-added, including 33 workflow files under .github/workflows/ and all referenced scripts (auto_bootstrap.py, integration_smoke.py, ci_orchestrator.py, etc.)

Post-restore fixes

• .devcontainer/devcontainer.json — merged two accidental top-level JSON objects into one valid object, removed // comments, combined all VS Code extensions, and updated the dev container image to 2-3.14-trixie
• .githooks/pre-commit — fixed set -e causing the failure-message branch to never execute; the test run is now bracketed with set +e/set -e so guidance is printed before exiting non-zero
• .github/workflows/makecode.yml — upgraded actions/checkout@v3 → @v4; added explicit actions/setup-node@v4 with node-version: '20' for reproducible builds
• .github/workflows/actionlint.yml — switched reporter from github-pr-check (PR-only) to github-check (works on both push and pull_request contexts); added permissions: checks: write
• .github/workflows/llm-maker-tests.yml — upgraded actions/setup-python@v4 → @v5 to align with the rest of the repository
• ## GitHub Copilot Chat.md — redacted sensitive diagnostic log content (account name, IP addresses, DNS results, system/network configuration); replaced with a safe summary pointing to the official troubleshooting docs

[sourcery-ai]

Hi @Copilot! 👋

Your private repo does not have access to Sourcery.

Please upgrade to continue using Sourcery ✨

[bryan-roe-bot]

Semgrep identified an issue in your code:
The strcpy family of functions do not provide the ability to limit or check buffer
sizes before copying to a destination buffer. This can lead to buffer overflows. Consider
using more secure alternatives such as strncpy and provide the correct limit to the
destination buffer and ensure the string is null terminated.

For more information please see: https://linux.die.net/man/3/strncpy

If developing for C Runtime Library (CRT), more secure versions of these functions should be
used, see:
https://learn.microsoft.com/en-us/cpp/c-runtime-library/reference/strncpy-s-strncpy-s-l-wcsncpy-s-wcsncpy-s-l-mbsncpy-s-mbsncpy-s-l?view=msvc-170

To resolve this comment:

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[Bryan-Roe]

@copilot /fix

[bryan-roe-bot]

Semgrep identified an issue in your code:
Be careful with flask.make_response(). If this response is rendered onto a webpage, this could create a cross-site scripting (XSS) vulnerability. flask.make_response() will not autoescape HTML. If you are rendering HTML, write your HTML in a template file and use flask.render_template() which will take care of escaping. If you are returning data from an API, consider using flask.jsonify().

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_{You can view more details about this finding in the Semgrep AppSec Platform.}

[Bryan-Roe]

@copilot /fix

[bryan-roe-bot]

Semgrep identified an issue in your code:
The application was found creating files in shared system temporary directories
(/tmp or /var/tmp) without using the tempfile.TemporaryFile function. Depending
on how the application uses this temporary file, an attacker may be able to create
symlinks that point to other files prior to the application creating or writing
to the target file, leading to unintended files being created or overwritten.

Example using tempfile.TemporaryFile to write a file:

import tempfile

# Open a new temporary file using a context manager
with tempfile.TemporaryFile() as fp:
    # Write some data to the temporary file
    fp.write(b'Some data')
    # Seek back to beginning of file
    fp.seek(0)
    # Read it
    data = fp.read()
# File is automatically closed/removed once we exit the with context

For more information on alternative tempfile functions see:

• https://docs.python.org/3/library/tempfile.html

To resolve this comment:

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_{You can view more details about this finding in the Semgrep AppSec Platform.}

[Bryan-Roe]

@copilot /fix

[bryan-roe-bot]

Semgrep identified an issue in your code:
This application allows user-controlled URLs to be passed directly to HTTP client libraries. This can result in Server-Side Request Forgery (SSRF). SSRF refers to an attack where the attacker can abuse functionality on the server to force it to make requests to other internal systems within your infrastructure that are not directly exposed to the internet. This allows the attacker to access internal resources they do not have direct access to.
Some risks of SSRF are:

• Access and manipulation of internal databases, APIs, or administrative panels - Ability to scan internal network architecture and services - Can be used to pivot attacks into the internal network - Circumvent network segregation and firewall rules
  To avoid this, try using hardcoded HTTP request calls or a whitelisting object to check whether the user input is trying to access allowed resources or not.
  Here is an example: var whitelist = [ "https://example.com", "https://example.com/sample" ] app.get('/ssrf/node-ssrf/axios/safe/3', function (req, res) { if(whitelist.includes(req.query.url)){ axios.get(url, {}) .then(function (response) { console.log(response); }) .catch(function (response) { console.log(response); }) } }); For more information on SSRF see OWASP: https://cheatsheetseries.owasp.org/cheatsheets/Server_Side_Request_Forgery_Prevention_Cheat_Sheet.html

Dataflow graph

flowchart LR
    classDef invis fill:white, stroke: none
    classDef default fill:#e7f5ff, color:#1c7fd6, stroke: none

    subgraph File0["<b>apps/chat/chat.js</b>"]
        direction LR
        %% Source

        subgraph Source
            direction LR

            v0["<a href=https://github.com/Bryan-Roe/Aria/blob/551a8cb1989e3198b6a0735d7c29464614c3984d/apps/chat/chat.js#L992 target=_blank style='text-decoration:none; color:#1c7fd6'>[Line: 992] nQubits</a>"]
        end
        %% Intermediate

        subgraph Traces0[Traces]
            direction TB

            v2["<a href=https://github.com/Bryan-Roe/Aria/blob/551a8cb1989e3198b6a0735d7c29464614c3984d/apps/chat/chat.js#L992 target=_blank style='text-decoration:none; color:#1c7fd6'>[Line: 992] nQubits</a>"]
        end
        %% Sink

        subgraph Sink
            direction LR

            v1["<a href=https://github.com/Bryan-Roe/Aria/blob/551a8cb1989e3198b6a0735d7c29464614c3984d/apps/chat/chat.js#L994 target=_blank style='text-decoration:none; color:#1c7fd6'>[Line: 994] fetch(QUANTUM_CIRCUIT_API, {
<br>            method: &apos;POST&apos;,
<br>            headers: { &apos;Content-Type&apos;: &apos;application/json&apos; },
<br>            body: JSON.stringify({
<br>                n_qubits: nQubits,
<br>                n_layers: nLayers,
<br>                entanglement: &apos;linear&apos;
<br>            })
<br>        })</a>"]
        end
    end
    %% Class Assignment
    Source:::invis
    Sink:::invis

    Traces0:::invis
    File0:::invis

    %% Connections

    Source --> Traces0
    Traces0 --> Sink

Loading

To resolve this comment:

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_{You can view more details about this finding in the Semgrep AppSec Platform.}

[Bryan-Roe]

@copilot /fix

[bryan-roe-bot]

Semgrep identified an issue in your code:
Errors should only be logged when handled. The code logs the error and propogates the exception, consider reducing the level to warning or info.

To resolve this comment:

🔧 No guidance has been designated for this issue. Fix according to your organization's approved methods.

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[Bryan-Roe]

@copilot /fix

[bryan-roe-bot]

Semgrep identified an issue in your code:
Untrusted user input in importlib.import_module() function allows an attacker to load arbitrary code. Avoid dynamic values in importlib.import_module() or use a whitelist to prevent running untrusted code.

To resolve this comment:

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_{You can view more details about this finding in the Semgrep AppSec Platform.}

[bryan-roe-bot]

Semgrep identified an issue in your code:
Starting a process with a shell; seems safe, but may be changed in the future, consider
rewriting without shell

To resolve this comment:

🔧 No guidance has been designated for this issue. Fix according to your organization's approved methods.

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_{You can view more details about this finding in the Semgrep AppSec Platform.}

[bryan-roe-bot]

Semgrep identified an issue in your code:
A hardcoded secret is identified. Store it properly in an environment variable.

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[bryan-roe-bot]

Semgrep identified an issue in your code:
The string method replaceAll is not supported in all versions of javascript, and is not supported by older browser versions. Consider using replace() with a regex as the first argument instead like mystring.replace(/bad/g, "good") instead of mystring.replaceAll("bad", "good") (https://discourse.threejs.org/t/replaceall-is-not-a-function/14585)

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[bryan-roe-bot]

Semgrep identified an issue in your code:
No validation of origin is done by the addEventListener API. It may be possible to exploit this flaw to perform Cross Origin attacks such as Cross-Site Scripting(XSS).

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[bryan-roe-bot]

Semgrep identified an issue in your code:
Scikit joblib uses pickle under the hood. Functions reliant on pickle can result in arbitrary code execution. Consider using skops instead.

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_{You can view more details about this finding in the Semgrep AppSec Platform.}

[bryan-roe-bot]

Semgrep identified an issue in your code:
The package cache was not deleted after running 'apt-get update', which increases the size of the image. Remove the package cache by appending '&& apt-get clean' at the end of apt-get command chain.

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[bryan-roe-bot]

Semgrep identified an issue in your code:
Service port is exposed on all interfaces

To resolve this comment:

🔧 No guidance has been designated for this issue. Fix according to your organization's approved methods.

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[bryan-roe-bot]

Semgrep identified an issue in your code:
Variable expansions must be double-quoted so as to prevent being split into multiple pieces according to whitespace or whichever separator is specified by the IFS variable. If you really wish to split the variable's contents, you may use a variable that starts with an underscore e.g. $_X instead of $X, and semgrep will ignore it. If what you need is an array, consider using a proper bash array.

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_{You can view more details about this finding in the Semgrep AppSec Platform.}

[bryan-roe-bot]

Semgrep identified an issue in your code:
The application was found calling the eval function OR Function()
constructor OR setTimeout() OR setInterval() methods. If the

variables or strings or functions passed to these methods contains user-supplied input, an adversary could attempt to execute arbitrary

JavaScript

code. This could lead to a full system compromise in Node applications or Cross-site Scripting

(XSS) in web applications.

To remediate this issue, remove all calls to above methods and consider alternative methods for

executing

the necessary business logic. There is almost no safe method of calling eval or other above stated sinks with

user-supplied input.

Instead, consider alternative methods such as using property accessors to dynamically access

values.

Example using property accessors to dynamically access an object's property:

// Define an object

const obj = {key1: 'value1', key2: 'value2'};

// Get key dynamically from user input

const key = getUserInput();

// Check if the key exists in our object and return it, or a default empty string

const value = (obj.hasOwnProperty(key)) ? obj[key] : '';

// Work with the value

For more information on why not to use eval, and alternatives see:

• https://developer.mozilla.org/en-US/docs/Web/JavaScript/Reference/Global_Objects/eval#never_use_eval!

Other References:

• https://developer.mozilla.org/en-US/docs/Web/JavaScript/Reference/Global_Objects/Function/Function

• https://developer.mozilla.org/en-US/docs/Web/API/setTimeout

• https://developer.mozilla.org/en-US/docs/Web/API/setInterval

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[bryan-roe-bot]

Semgrep identified an issue in your code:
Avoid DML statements inside loops to avoid hitting the DML governor limit. Instead, try to batch up the data into a list and invoke your DML once on that list of data outside the loop.

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_{You can view more details about this finding in the Semgrep AppSec Platform.}

[bryan-roe-bot]

Semgrep identified an issue in your code:
Avoid using pickle, which is known to lead to code execution vulnerabilities. When unpickling, the serialized data could be manipulated to run arbitrary code. Instead, consider serializing the relevant data as JSON or a similar text-based serialization format.

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_{You can view more details about this finding in the Semgrep AppSec Platform.}

[bryan-roe-bot]

Semgrep identified an issue in your code:
Avoid using pickle, which is known to lead to code execution vulnerabilities. When unpickling, the serialized data could be manipulated to run arbitrary code. Instead, consider serializing the relevant data as JSON or a similar text-based serialization format.

To resolve this comment:

🔧 No guidance has been designated for this issue. Fix according to your organization's approved methods.

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[bryan-roe-bot]

Semgrep identified an issue in your code:
subprocess call - check for execution of untrusted input

To resolve this comment:

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[bryan-roe-bot]

Semgrep identified an issue in your code:
The application was found using pickle which is vulnerable to deserialization attacks.
Deserialization attacks exploit the process of reading serialized data and turning it back
into an object. By constructing malicious objects and serializing them, an adversary may
attempt to:

• Inject code that is executed upon object construction, which occurs during the
  deserialization process.
• Exploit mass assignment by including fields that are not normally a part of the serialized
  data but are read in during deserialization.

Consider safer alternatives such as serializing data in the JSON format. Ensure any format
chosen allows the application to specify exactly which object types are allowed to be deserialized.

To protect against mass assignment, only allow deserialization of the specific fields that are
required. If this is not easily done, consider creating an intermediary type that
can be serialized with only the necessary fields exposed.

Example JSON deserializer using an intermediary type that is validated against a schema to ensure
it is safe from mass assignment:

import jsonschema

# Create a schema to validate our user-supplied input against
# an intermediary object
intermediary_schema = {
    "type" : "object",
    "properties" :  {
        "name": {"type" : "string"}
    },
    "required": ["name"],
    # Protect against random properties being added to the object
    "additionalProperties": False,
}
# If a user attempted to add "'is_admin': True" it would cause a validation error
intermediary_object = {'name': 'test user'}

try:
    # Validate the user supplied intermediary object against our schema
    jsonschema.validate(instance=intermediary_object, schema=intermediary_schema)
    user_object = {'user':
        {
            # Assign the deserialized data from intermediary object
            'name': intermediary_object['name'],
            # Add in protected data in object definition (or set it from a class constructor)
            'is_admin': False,
        }
    }
    # Work with the user_object
except jsonschema.exceptions.ValidationError as ex:
    # Gracefully handle validation errors
    # ...

For more details on deserialization attacks in general, see OWASP's guide:

• https://cheatsheetseries.owasp.org/cheatsheets/Deserialization_Cheat_Sheet.html

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_{You can view more details about this finding in the Semgrep AppSec Platform.}

[bryan-roe-bot]

Semgrep identified an issue in your code:
Possibility of prototype polluting assignment detected. By adding or modifying attributes of an object prototype, it is possible to create attributes that exist on every object, or replace critical attributes with malicious ones. This can be problematic if the software depends on existence or non-existence of certain attributes, or uses pre-defined attributes of object prototype (such as hasOwnProperty, toString or valueOf). Possible mitigations might be: freezing the object prototype, using an object without prototypes (via Object.create(null) ), blocking modifications of attributes that resolve to object prototype, using Map instead of object.

To resolve this comment:

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_{You can view more details about this finding in the Semgrep AppSec Platform.}

[bryan-roe-bot]

Semgrep identified an issue in your code:
This application allows user-controlled URLs to be passed directly to HTTP client libraries. This can result in Server-Side Request Forgery (SSRF). SSRF refers to an attack where the attacker can abuse functionality on the server to force it to make requests to other internal systems within your infrastructure that are not directly exposed to the internet. This allows the attacker to access internal resources they do not have direct access to.
Some risks of SSRF are:

• Access and manipulation of internal databases, APIs, or administrative panels - Ability to scan internal network architecture and services - Can be used to pivot attacks into the internal network - Circumvent network segregation and firewall rules
  To avoid this, try using hardcoded HTTP request calls or a whitelisting object to check whether the user input is trying to access allowed resources or not.
  Here is an example: var whitelist = [ "https://example.com", "https://example.com/sample" ] app.get('/ssrf/node-ssrf/axios/safe/3', function (req, res) { if(whitelist.includes(req.query.url)){ axios.get(url, {}) .then(function (response) { console.log(response); }) .catch(function (response) { console.log(response); }) } }); For more information on SSRF see OWASP: https://cheatsheetseries.owasp.org/cheatsheets/Server_Side_Request_Forgery_Prevention_Cheat_Sheet.html

Dataflow graph

flowchart LR
    classDef invis fill:white, stroke: none
    classDef default fill:#e7f5ff, color:#1c7fd6, stroke: none

    subgraph File0["<b>apps/aria/aria_controller.js</b>"]
        direction LR
        %% Source

        subgraph Source
            direction LR

            v0["<a href=https://github.com/Bryan-Roe/Aria/blob/551a8cb1989e3198b6a0735d7c29464614c3984d/apps/aria/aria_controller.js#L930 target=_blank style='text-decoration:none; color:#1c7fd6'>[Line: 930] tag</a>"]
        end
        %% Intermediate

        subgraph Traces0[Traces]
            direction TB

            v2["<a href=https://github.com/Bryan-Roe/Aria/blob/551a8cb1989e3198b6a0735d7c29464614c3984d/apps/aria/aria_controller.js#L930 target=_blank style='text-decoration:none; color:#1c7fd6'>[Line: 930] tag</a>"]

            v3["<a href=https://github.com/Bryan-Roe/Aria/blob/551a8cb1989e3198b6a0735d7c29464614c3984d/apps/aria/aria_controller.js#L932 target=_blank style='text-decoration:none; color:#1c7fd6'>[Line: 932] match</a>"]

            v4["<a href=https://github.com/Bryan-Roe/Aria/blob/551a8cb1989e3198b6a0735d7c29464614c3984d/apps/aria/aria_controller.js#L938 target=_blank style='text-decoration:none; color:#1c7fd6'>[Line: 938] ]</a>"]

            v5["<a href=https://github.com/Bryan-Roe/Aria/blob/551a8cb1989e3198b6a0735d7c29464614c3984d/apps/aria/aria_controller.js#L938 target=_blank style='text-decoration:none; color:#1c7fd6'>[Line: 938] paramRaw</a>"]

            v6["<a href=https://github.com/Bryan-Roe/Aria/blob/551a8cb1989e3198b6a0735d7c29464614c3984d/apps/aria/aria_controller.js#L942 target=_blank style='text-decoration:none; color:#1c7fd6'>[Line: 942] param</a>"]

            v7["<a href=https://github.com/Bryan-Roe/Aria/blob/551a8cb1989e3198b6a0735d7c29464614c3984d/apps/aria/aria_controller.js#L998 target=_blank style='text-decoration:none; color:#1c7fd6'>[Line: 998] ]</a>"]

            v8["<a href=https://github.com/Bryan-Roe/Aria/blob/551a8cb1989e3198b6a0735d7c29464614c3984d/apps/aria/aria_controller.js#L998 target=_blank style='text-decoration:none; color:#1c7fd6'>[Line: 998] ]</a>"]

            v9["<a href=https://github.com/Bryan-Roe/Aria/blob/551a8cb1989e3198b6a0735d7c29464614c3984d/apps/aria/aria_controller.js#L998 target=_blank style='text-decoration:none; color:#1c7fd6'>[Line: 998] objectName</a>"]

            v10["<a href=https://github.com/Bryan-Roe/Aria/blob/551a8cb1989e3198b6a0735d7c29464614c3984d/apps/aria/aria_controller.js#L999 target=_blank style='text-decoration:none; color:#1c7fd6'>[Line: 999] addObject</a>"]

            v11["<a href=https://github.com/Bryan-Roe/Aria/blob/551a8cb1989e3198b6a0735d7c29464614c3984d/apps/aria/aria_controller.js#L2220 target=_blank style='text-decoration:none; color:#1c7fd6'>[Line: 2220] objectName</a>"]

            v12["<a href=https://github.com/Bryan-Roe/Aria/blob/551a8cb1989e3198b6a0735d7c29464614c3984d/apps/aria/aria_controller.js#L2256 target=_blank style='text-decoration:none; color:#1c7fd6'>[Line: 2256] toggleObject</a>"]

            v13["<a href=https://github.com/Bryan-Roe/Aria/blob/551a8cb1989e3198b6a0735d7c29464614c3984d/apps/aria/aria_controller.js#L149 target=_blank style='text-decoration:none; color:#1c7fd6'>[Line: 149] objectId</a>"]

            v14["<a href=https://github.com/Bryan-Roe/Aria/blob/551a8cb1989e3198b6a0735d7c29464614c3984d/apps/aria/aria_controller.js#L168 target=_blank style='text-decoration:none; color:#1c7fd6'>[Line: 168] sendObjectUpdate</a>"]

            v15["<a href=https://github.com/Bryan-Roe/Aria/blob/551a8cb1989e3198b6a0735d7c29464614c3984d/apps/aria/aria_controller.js#L1942 target=_blank style='text-decoration:none; color:#1c7fd6'>[Line: 1942] objectId</a>"]

            v16["<a href=https://github.com/Bryan-Roe/Aria/blob/551a8cb1989e3198b6a0735d7c29464614c3984d/apps/aria/aria_controller.js#L1954 target=_blank style='text-decoration:none; color:#1c7fd6'>[Line: 1954] objPayload</a>"]

            v17["<a href=https://github.com/Bryan-Roe/Aria/blob/551a8cb1989e3198b6a0735d7c29464614c3984d/apps/aria/aria_controller.js#L1958 target=_blank style='text-decoration:none; color:#1c7fd6'>[Line: 1958] payload</a>"]
        end
            v2 --> v3
            v3 --> v4
            v4 --> v5
            v5 --> v6
            v6 --> v7
            v7 --> v8
            v8 --> v9
            v9 --> v10
            v10 --> v11
            v11 --> v12
            v12 --> v13
            v13 --> v14
            v14 --> v15
            v15 --> v16
            v16 --> v17
        %% Sink

        subgraph Sink
            direction LR

            v1["<a href=https://github.com/Bryan-Roe/Aria/blob/551a8cb1989e3198b6a0735d7c29464614c3984d/apps/aria/aria_controller.js#L1960 target=_blank style='text-decoration:none; color:#1c7fd6'>[Line: 1960] fetch(&apos;/api/aria/object&apos;, {
<br>            method: &apos;POST&apos;,
<br>            headers: { &apos;Content-Type&apos;: &apos;application/json&apos; },
<br>            body: JSON.stringify(payload)
<br>        })</a>"]
        end
    end
    %% Class Assignment
    Source:::invis
    Sink:::invis

    Traces0:::invis
    File0:::invis

    %% Connections

    Source --> Traces0
    Traces0 --> Sink

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[sourcery-ai]

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Please upgrade to continue using Sourcery ✨

[Copilot]

Pull request overview

Note

Copilot was unable to run its full agentic suite in this review.

Restores the repository after an accidental empty-tree commit wiped the working tree, reintroducing source, GitHub Actions workflows, and repo configuration so CI can run again.

Changes:

• Re-added GitHub Actions workflows and a reusable composite action for Python environment setup.
• Restored repo automation/configuration under .github/ (prompts, skills, instructions, hooks, templates, labeler, CODEOWNERS).
• Restored developer tooling/config files (devcontainer, githooks, ignore files, Azure ML specs).

Reviewed changes

Copilot reviewed 202 out of 1681 changed files in this pull request and generated 8 comments.

Show a summary per file

File	Description
.github/workflows/markdown-quality.yml	Restores Markdown lint workflow to bring back docs quality checks.
.github/workflows/makecode.yml	Restores MakeCode build workflow.
.github/workflows/llm-maker-tests.yml	Restores llm-maker pytest workflow for that subproject.
.github/workflows/integration-contract-gate.yml	Restores contract gate workflow for integration scripts/status artifacts.
.github/workflows/e2e-tests.yml	Restores quick Aria regression suite jobs (unit/integration + UI).
.github/workflows/devcontainer-ci.yml	Restores devcontainer build/test CI.
.github/workflows/dependency-review.yml	Restores dependency review gate on PRs.
.github/workflows/dependabot-automerge.yml	Restores Dependabot auto-approval/merge automation.
.github/workflows/codeql.yml	Restores CodeQL scanning workflow.
.github/workflows/code-quality.yml	Restores linting and dependency audit workflows.
.github/workflows/broken-links.yml	Restores docs link checking workflow.
.github/workflows/azureml-train.yml	Restores manual AzureML training submission workflow.
.github/workflows/auto-validation.yml	Restores orchestrator config validation workflow.
.github/workflows/artifact-lifecycle.yml	Restores scheduled/manual artifact cleanup workflow.
.github/workflows/api-health-smoke.yml	Restores API smoke checks + artifact upload.
.github/workflows/actionlint.yml	Restores workflow linting for maintaining GA YAML quality.
.github/workflows/README.md	Documents restored workflows and intended usage patterns.
.github/skills/**/SKILL.md	Restores skill docs used for consistent debugging/refactor/ops workflows.
.github/prompts/*.prompt.md	Restores prompt definitions for repo-specific agent workflows.
.github/labeler.yml	Restores PR auto-labeling rules.
.github/instructions/*.instructions.md	Restores scoped coding/testing instructions for key areas.
.github/hooks/*.json	Restores hook configuration for guardrails (secrets, scope drift, etc.).
.github/actions/setup-python-env/action.yml	Restores composite action for consistent Python setup/install/caching in CI.
.github/PULL_REQUEST_TEMPLATE.md	Restores PR template to standardize summaries/testing notes.
.github/ISSUE_TEMPLATE/feature_request.md	Restores GitHub issue template (feature request).
.github/ISSUE_TEMPLATE/bug_report.md	Restores GitHub issue template (bug report).
.github/FUNDING.yml	Restores funding configuration.
.github/CODEOWNERS	Restores default repository code ownership.
.githooks/pre-commit.ps1	Restores Windows pre-commit test hook.
.githooks/pre-commit	Restores bash pre-commit test hook.
.githooks/README.md	Documents installation/usage of restored githooks.
.funcignore	Restores Azure Functions packaging ignore list.
.foundry/.deployment.json	Restores Foundry deployment metadata.
.env.example	Restores example env var template for local dev.
.dockerignore	Restores Docker ignore patterns.
.devcontainer/devcontainer.json	Restores devcontainer configuration for local dev environment.
.azureml/job_multi_20251125T055919Z.yaml	Restores generated AzureML command job spec.
.azureml/job_multi_20251125T012559Z.yaml	Restores generated AzureML command job spec.
.azureml/job_multi_20251125T012515Z.yaml	Restores generated AzureML command job spec.
.azureml/job_dummy.yaml	Restores placeholder AzureML job spec.
.azureml/environment.yml	Restores AzureML environment definition.
## GitHub Copilot Chat.md	Restores captured Copilot Chat diagnostic log (see security note below).

---

💡 Add Copilot custom instructions for smarter, more guided reviews. Learn how to get started.

[Copilot]

This file is not valid JSON (it contains two top-level objects and // comments). Dev Containers expects a single JSON object, so this will break devcontainer startup. Keep one configuration object (merge the desired fields and images into one) and remove comments or relocate them to a separate README.

Suggested change

	"ms-azuretools.vscode-docker"
	]
	}
	}
	}
	// For format details, see https://aka.ms/devcontainer.json. For config options, see the
	// README at: https://github.com/devcontainers/templates/tree/main/src/python
	{
	"name": "Python 3",
	// Or use a Dockerfile or Docker Compose file. More info: https://containers.dev/guide/dockerfile
	"image": "mcr.microsoft.com/devcontainers/python:2-3.14-trixie",
	"customizations": {
	"vscode": {
	"extensions": [
	"ms-windows-ai-studio.windows-ai-studio",
	"GitHub.copilot-chat"
	]
	}
	}
	// Features to add to the dev container. More info: https://containers.dev/features.
	// "features": {},
	// Use 'forwardPorts' to make a list of ports inside the container available locally.
	// "forwardPorts": [],
	// Use 'postCreateCommand' to run commands after the container is created.
	// "postCreateCommand": "pip3 install --user -r requirements.txt",
	// Configure tool-specific properties.
	// "customizations": {},
	// Uncomment to connect as root instead. More info: https://aka.ms/dev-containers-non-root.
	// "remoteUser": "root"
	"ms-azuretools.vscode-docker",
	"ms-windows-ai-studio.windows-ai-studio",
	"GitHub.copilot-chat"
	]
	}
	}

[Copilot]

env: is currently nested under with: (same indentation level as with:'s keys), which means GitHub Actions will treat it as an invalid input rather than setting environment variables for the step. Move env: to be a sibling of with: (step-level) so GITHUB_TOKEN is actually set for the action.

Suggested change

	GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
	GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

[Copilot]

set -e causes the script to exit immediately when the test command fails, so the failure-message branch never runs (and the $? check is effectively dead code in failure cases). Capture the test exit code (or temporarily disable -e around the test run) so the hook can print the intended guidance before exiting non-zero.

[Copilot]

This workflow relies on npx makecode but does not set up a specific Node.js version (and uses actions/checkout@v3). For reliability/reproducibility, add an explicit Node setup step (with caching if appropriate) and upgrade checkout to actions/checkout@v4 to align with the rest of the workflows.

Suggested change

	- uses: actions/checkout@v3
	with:
	submodules: recursive
	- uses: actions/checkout@v4
	with:
	submodules: recursive
	- uses: actions/setup-node@v4
	with:
	node-version: '20'

[Copilot]

This workflow runs on push and workflow_dispatch, but reviewdog's github-pr-check reporter is PR-oriented and can fail or behave unexpectedly when there is no PR context. Consider either (a) restricting this workflow to pull_request only, or (b) switching to a reporter that works on pushes (and adding the minimal required permissions for creating check runs if needed).

[Copilot]

Most workflows here use actions/setup-python@v5 (and the repo has a composite action that uses v5). To reduce version skew and benefit from the newer action, update this to actions/setup-python@v5 (or reuse ./.github/actions/setup-python-env).

Suggested change

	uses: actions/setup-python@v4
	uses: actions/setup-python@v5

[Copilot]

This appears to be a local diagnostic/support log and includes potentially sensitive environment details (account name, network/DNS behavior, internal configuration). Consider removing it from the repository (or moving it to a private support artifact), or at minimum redact identifiers and any environment-specific details before committing.

Suggested change

	- Extension: 0.41.2 (prod)
	- VS Code: 1.113.0 (cfbea10c5ffb233ea9177d34726e6056e89913dc)
	- OS: linux 6.6.87.2-microsoft-standard-WSL2 x64
	- Remote Name: dev-container
	- Extension Kind: Workspace
	- GitHub Account: Bryan-Roe
	## Network
	User Settings:
	```json
	"http.systemCertificatesNode": true,
	"http.experimental.systemCertificatesV2": true,
	"github.copilot.advanced.debug.useElectronFetcher": false,
	"github.copilot.advanced.debug.useNodeFetcher": true,
	"github.copilot.advanced.debug.useNodeFetchFetcher": false
	```
	Connecting to https://api.github.com:
	- DNS ipv4 Lookup: 140.82.116.6 (37 ms)
	- DNS ipv6 Lookup: Error (18 ms): getaddrinfo ENOTFOUND api.github.com
	- Proxy URL: None (1 ms)
	- Electron fetch: Unavailable
	- Node.js https (configured): HTTP 200 (2096 ms)
	- Node.js fetch (active): HTTP 200 (306 ms)
	Connecting to https://api.individual.githubcopilot.com/_ping:
	- DNS ipv4 Lookup: 140.82.114.21 (8 ms)
	- DNS ipv6 Lookup: Error (6 ms): getaddrinfo ENOTFOUND api.individual.githubcopilot.com
	- Proxy URL: None (0 ms)
	- Electron fetch: Unavailable
	- Node.js https (configured): HTTP 200 (471 ms)
	- Node.js fetch (active): HTTP 200 (134 ms)
	Connecting to https://proxy.individual.githubcopilot.com/_ping:
	- DNS ipv4 Lookup: 138.91.182.224 (10 ms)
	- DNS ipv6 Lookup: Error (7 ms): getaddrinfo ENOTFOUND proxy.individual.githubcopilot.com
	- Proxy URL: None (0 ms)
	- Electron fetch: Unavailable
	- Node.js https (configured): HTTP 200 (246 ms)
	- Node.js fetch (active): HTTP 200 (202 ms)
	Connecting to https://mobile.events.data.microsoft.com: HTTP 404 (771 ms)
	Connecting to https://dc.services.visualstudio.com: HTTP 404 (548 ms)
	Connecting to https://copilot-telemetry.githubusercontent.com/_ping: HTTP 200 (382 ms)
	Connecting to https://telemetry.individual.githubcopilot.com/_ping: HTTP 200 (564 ms)
	Connecting to https://default.exp-tas.com: HTTP 400 (527 ms)
	Number of system certificates: 414
	## Documentation
	In corporate networks: [Troubleshooting firewall settings for GitHub Copilot](https://docs.github.com/en/copilot/troubleshooting-github-copilot/troubleshooting-firewall-settings-for-github-copilot).
	This file previously contained a local diagnostic/support log generated from a development environment.
	The detailed log has been removed from version control because it included environment-specific and potentially sensitive information such as account identifiers, system configuration, and network diagnostics.
	## Documentation
	For troubleshooting GitHub Copilot connectivity in corporate networks, see [Troubleshooting firewall settings for GitHub Copilot](https://docs.github.com/en/copilot/troubleshooting-github-copilot/troubleshooting-firewall-settings-for-github-copilot).

[Copilot]

This appears to be a local diagnostic/support log and includes potentially sensitive environment details (account name, network/DNS behavior, internal configuration). Consider removing it from the repository (or moving it to a private support artifact), or at minimum redact identifiers and any environment-specific details before committing.

[Bryan-Roe]

@copilot apply changes based on this feedback

[Copilot]

Done in commit 5361ec1. Replaced the sensitive diagnostic log with a safe summary that removes all environment-specific details (account name, IP addresses, DNS results, system/network config) and points to the official troubleshooting docs instead.

[Copilot]

@Bryan-Roe Unfortunately I hit an unexpected error while processing your comment. I've automatically reported this to GitHub.

You can ask me to try again later by mentioning me in a new comment.

If you want to contact GitHub about this error, please mention the following identifier so they can better serve you: ecf9e0ef-8103-4754-86ec-73d84f05a5dc

Sorry for the inconvenience!

[Bryan-Roe]

@copilot apply changes based on the comments in this thread

[chatgpt-codex-connector]

💡 Codex Review

Here are some automated review suggestions for this pull request.

Reviewed commit: b46bdfef3c

ℹ️ About Codex in GitHub

Your team has set up Codex to review pull requests in this repo. Reviews are triggered when you

• Open a pull request for review
• Mark a draft as ready
• Comment "@codex review".

If Codex has suggestions, it will comment; otherwise it will react with 👍.

Codex can also answer questions or update the PR. Try commenting "@codex address that feedback".

[chatgpt-codex-connector]

Import sys before using sys.exit in demo script

This change replaces exit(1) with sys.exit(1), but the module still does not import sys, so any non-200 response path now raises NameError instead of terminating cleanly. In practice, when /api/datasets or /api/train/start fails, the script will crash with an exception and mask the actual failure condition.

Useful? React with 👍 / 👎.

[chatgpt-codex-connector]

💡 Codex Review

Here are some automated review suggestions for this pull request.

Reviewed commit: 16570d0cb1

ℹ️ About Codex in GitHub

Your team has set up Codex to review pull requests in this repo. Reviews are triggered when you

• Open a pull request for review
• Mark a draft as ready
• Comment "@codex review".

If Codex has suggestions, it will comment; otherwise it will react with 👍.

Codex can also answer questions or update the PR. Try commenting "@codex address that feedback".

[chatgpt-codex-connector]

Fix invalid string expression that breaks module parsing

The expression print("=""*70 + "\n") is syntactically invalid Python, so importing or executing privacy_first_ai.py fails immediately with a SyntaxError before any privacy workflow runs. This makes the entire example module unusable in environments that load it as a script or import it for demonstrations.

Useful? React with 👍 / 👎.

[chatgpt-codex-connector]

Remove stray comma in requests call argument list

This requests.post call has a standalone leading comma before timeout, which is invalid syntax and prevents the file from being parsed. As a result, the test module cannot be imported or run at all (and the same malformed pattern appears again in execute_mode), so the auto-execute smoke tests are effectively broken.

Useful? React with 👍 / 👎.

[chatgpt-codex-connector]

Codex usage limits have been reached for code reviews. Please check with the admins of this repo to increase the limits by adding credits.
Credits must be used to enable repository wide code reviews.

[github-actions]

🔴 Coverage — ba95a40

Metric	Value
Total coverage	56.5%
Minimum threshold	60%

Updated on every push · 2026-04-11

[Copilot]

@copilot apply changes based on the comments in this thread

All review feedback applied in commit 5361ec1:

• .devcontainer/devcontainer.json — merged two top-level objects into one valid JSON, removed // comments, combined all four extensions, updated image to 2-3.14-trixie
• .githooks/pre-commit — fixed set -e dead-code issue by capturing exit code with set +e/TEST_EXIT_CODE=$?/set -e so the failure message branch can actually run
• .github/workflows/makecode.yml — upgraded checkout@v3 → @v4, added setup-node@v4 with node-version: '20'
• .github/workflows/actionlint.yml — changed reporter from github-pr-check to github-check (works on push context too), added permissions: checks: write
• .github/workflows/llm-maker-tests.yml — upgraded setup-python@v4 → @v5
• ## GitHub Copilot Chat.md — redacted sensitive diagnostic log content
• .github/workflows/broken-links.yml — env: was already correctly placed at step level; no change needed

[chatgpt-codex-connector]

You have reached your Codex usage limits for code reviews. You can see your limits in the Codex usage dashboard.

[bryan-roe-bot]

Semgrep identified an issue in your code:
Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8").

To resolve this comment:

🔧 No guidance has been designated for this issue. Fix according to your organization's approved methods.

💬 Ignore this finding

Reply with Semgrep commands to ignore this finding.

• /fp <comment> for false positive
• /ar <comment> for acceptable risk
• /other <comment> for all other reasons

Alternatively, triage in Semgrep AppSec Platform to ignore the finding created by unspecified-open-encoding.

_{You can view more details about this finding in the Semgrep AppSec Platform.}

[bryan-roe-bot]

Semgrep identified an issue in your code:
Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8").

To resolve this comment:

🔧 No guidance has been designated for this issue. Fix according to your organization's approved methods.

💬 Ignore this finding

Reply with Semgrep commands to ignore this finding.

• /fp <comment> for false positive
• /ar <comment> for acceptable risk
• /other <comment> for all other reasons

Alternatively, triage in Semgrep AppSec Platform to ignore the finding created by unspecified-open-encoding.

_{You can view more details about this finding in the Semgrep AppSec Platform.}

[bryan-roe-bot]

Semgrep identified an issue in your code:
Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8").

To resolve this comment:

🔧 No guidance has been designated for this issue. Fix according to your organization's approved methods.

💬 Ignore this finding

Reply with Semgrep commands to ignore this finding.

• /fp <comment> for false positive
• /ar <comment> for acceptable risk
• /other <comment> for all other reasons

Alternatively, triage in Semgrep AppSec Platform to ignore the finding created by unspecified-open-encoding.

_{You can view more details about this finding in the Semgrep AppSec Platform.}

[bryan-roe-bot]

Semgrep found 33 rule findings:

• ai-projects/lmstudio-mcp/privacy_first_ai.py
  • L343 - Triage
  • L344 - Triage
  • L345 - Triage
  • L368 - Triage
  • L386 - Triage
  • L387 - Triage
  • L388 - Triage
  • L410 - Triage
  • L424 - Triage
  • L425 - Triage
  • 23 more - Triage

Semgrep found a match

[bryan-roe-bot]

Semgrep identified an issue in your code:
function check is defined inside a function but never used

To resolve this comment:

🔧 No guidance has been designated for this issue. Fix according to your organization's approved methods.

💬 Ignore this finding

Reply with Semgrep commands to ignore this finding.

• /fp <comment> for false positive
• /ar <comment> for acceptable risk
• /other <comment> for all other reasons

Alternatively, triage in Semgrep AppSec Platform to ignore the finding created by useless-inner-function.

_{You can view more details about this finding in the Semgrep AppSec Platform.}