Fix some script + make target discrepancies post refactor

[Apmats]

Not related to any specific issue

Summary

The monorepo restructure in #3721 moved the connector service into app/connectors_service/, but several file path references across Makefiles and stack scripts were not updated. This caused broken behavior for users running connectors from source:

• make run from the repo root silently ignored the user's config.yml, falling back to service_cli.py's default path inside app/connectors_service/. This produced a confusing Cannot connect to host localhost:9200 error even with a valid cloud config at the repo root.
• The scripts/stack/ development scripts referenced stale paths for VERSION, config.yml.example, and the connectors CLI binary — all of which moved during the restructure.
• run-stack.sh --no-connectors still prompted for the connector configurator.
• The stack scripts themselves were left at the repo root despite being specific to the connector service.

Changes

Makefile wiring for make run

• Root Makefile: added a config.yml target (copies from example if missing) and updated run to pass CONFIG_FILE=$(CURDIR)/config.yml to the inner Makefile.
• app/connectors_service/Makefile: added CONFIG_FILE ?= config.yml and updated run to pass -c $(CONFIG_FILE) explicitly. When called from root, it receives the absolute path; when called directly, it defaults to the local config.yml.

Move scripts/stack/ into app/connectors_service/scripts/stack/

Per review feedback, relocated the stack scripts to live alongside the service they belong to. This simplifies all internal path references because PROJECT_ROOT (computed as two directories up from the script location) now naturally resolves to app/connectors_service/ — eliminating the need for app/connectors_service/ prefixes throughout.

Script fixes

• copy-config.sh: removed the intermediary cp that created a ghost config.yml at PROJECT_ROOT; now points directly at config.yml.example.
• configure-connectors.sh: fixed the connectors CLI path (bin/connectors → .venv/bin/connectors).
• run-stack.sh: moved config copy, configurator prompt, and connector startup inside the no_connectors == false block.

Reference updates

• .gitignore: updated connectors-config path; added root config.yml to ignore list.
• README.md, docs/CLI.md, stack README.md: updated all scripts/stack/ links and command examples to the new location.

Checklists

Pre-Review Checklist

• this PR does NOT contain credentials of any kind, such as API keys or username/passwords (double check config.yml.example)
• this PR has a meaningful title
• this PR links to all relevant github issues that it fixes or partially addresses
• if there is no GH issue, please create it. Each PR should have a link to an issue
• this PR has a thorough description
• Covered the changes with automated tests
• Tested the changes locally
• Added a label for each target release version (example: v7.13.2, v7.14.0, v8.0.0)
• For bugfixes: backport safely to all minor branches still receiving patch releases
• Considered corresponding documentation changes
• Contributed any configuration settings changes to the configuration reference
• if you added or changed Rich Configurable Fields for a Native Connector, you made a corresponding PR in Kibana

Changes Requiring Extra Attention

N/A — no security changes, no new dependencies.

Related Pull Requests

• Restructure Connectors project #3721 — Restructure Connectors project (introduced the monorepo layout)
• Kibana-side instructions may also need updating to reference app/connectors_service/config.yml for the "run from source" path

Release Note

Fixed broken file path references in Makefiles and stack scripts that were not updated during the monorepo restructure (#3721). Users running connectors from source who were experiencing Cannot connect to host localhost:9200 errors (despite having a valid config.yml at the repo root) will find that make run now correctly picks up their configuration. The scripts/stack/ development scripts have also been relocated to app/connectors_service/scripts/stack/ and fixed to reference correct post-restructure paths. These fixes will take effect after merging to the corresponding branches and are not strictly tied to a specific release.

[lorenabalan]

Where's PROJECT_ROOT defined? I thought that was modified to point to app/connectors_service but I might be misremembering!

[Apmats]

It's under scripts/stack/set-env.sh - I didn't think about this subject at all, but you might still have feelings on this since this is largely your baby 😁 - do you think we should refactor where these scripts live too?

[lorenabalan]

I wouldn't be opposed to it, I'm not sure there was any explicit reason why they were left behind. If they're not used in CI or root-level Makefile then it would make sense to me to move them. Looking at them they all seem related to the service itself anw.

[Apmats]

Alright. Moved and adjusted stuff around that move.

[Apmats]

This is still happening somehow - will need a fresh ✅ after the last changes. @lorenabalan have a 👀