dvc status: reports "no data tracked" when using `**` globbing patterns in `.gitignore`

Bug Report

Description

dvc status fails to recognize .dvc files when .gitignore uses ** globbing patterns with negation rules (e.g., data/raw/** followed by !data/raw/**/*.dvc). DVC reports "There are no data or pipelines tracked in this project yet" even though:

.dvc files are correctly committed to Git
dvc add succeeds without errors
The cache is properly populated
Individual file queries work (dvc status file.dvc)

This causes dvc push to silently skip pushing data to remotes, as DVC believes no files are tracked.

Reproduce

Initialize a Git repository and DVC:

git init
dvc init

Create a .gitignore with the following patterns:

# Ignore all data files
data/raw/**
data/interim/**
data/processed/**

# But keep DVC metafiles
!data/raw/**/*.dvc
!data/interim/**/*.dvc
!data/processed/**/*.dvc

.dvc/cache/

Add a data file:

mkdir -p data/raw
echo "test data" > data/raw/example.nc
dvc add data/raw/example.nc
git add data/raw/example.nc.dvc .gitignore
git commit -m "Add data file"

Check DVC status:

dvc status
dvc status --cloud

Verify the issue:

# This shows the file is NOT in DVC's index
dvc status
# Output: "There are no data or pipelines tracked in this project yet."

# But individual queries work
dvc status data/raw/example.nc.dvc
# Output: Shows file status correctly

# Git correctly tracks the file
git ls-files "*.dvc"
# Output: data/raw/example.nc.dvc

# Push appears to succeed but does nothing
dvc push
# Output: "Everything is up to date." (even if remote is empty)

Expected

dvc status should recognize all .dvc files tracked in Git and report their status correctly, regardless of .gitignore globbing patterns used. The command should output the status of tracked data files, and dvc push should push data to the remote when needed.

Environment information

Output of dvc doctor:

$ dvc doctor

DVC version: 3.66.1 (conda)
---------------------------
Platform: Python 3.12.12 on Windows-11-10.0.26200-SP0
Subprojects:
        dvc_data = 3.18.2
        dvc_objects = 5.2.0
        dvc_render = 1.0.2
        dvc_task = 0.40.2
        scmrepo = 3.6.1
Supports:
        http (aiohttp = 3.13.3, aiohttp-retry = 2.9.1),
        https (aiohttp = 3.13.3, aiohttp-retry = 2.9.1)
Config:
        Global: C:\Users\username\AppData\Local\iterative\dvc
        System: C:\ProgramData\iterative\dvc
Cache types: <https://error.dvc.org/no-dvc-cache>
Caches: local
Remotes: local
Workspace directory: NTFS on C:\
Repo: dvc, git

Additional Information (if any):

Package manager: Pixi 0.63.2
Git version: 2.45.2.windows.1
Cache type configured: copy

Verbose output showing DVC doesn't find stages:

$ dvc status --cloud -vv
2026-02-05 17:22:39,507 TRACE: Namespace(...)
2026-02-05 17:22:40,518 TRACE: 1.61 ms in collecting stages from [project directories]
There are no data or pipelines tracked in this project yet.

Python verification that index is empty:

>>> import dvc.repo
>>> repo = dvc.repo.Repo('.')
>>> repo.index.stages
[]  # Empty despite .dvc files existing in Git

Workaround that fixes the issue:
Replace the ** globbing patterns with specific file patterns:

# Instead of:
# data/raw/**
# !data/raw/**/*.dvc

# Use:
data/raw/*.nc
data/interim/*.parquet
data/processed/*.csv

After changing .gitignore:

dvc add data/raw/*.nc --force  # Re-cache files
dvc status  # Now correctly shows tracked files
dvc push    # Successfully pushes to remote

Impact: This is a critical silent failure that affects users following common patterns for ignoring data directories while keeping DVC metadata. The issue took 4 hours to debug because there are no warnings or errors indicating that .dvc files exist but aren't being tracked by DVC's index.

Reproduce the case with the .gitignore patterns and dvc status, then start at dvc.repo.Repo and its repo.index.stages entry point, using the verbose stage-collection output to trace discovery. Done means tracked .dvc files are included in dvc status despite the ** negation rules, and dvc push no longer skips their data.