chore(github): rebuild the issue, discussion and automation setup

.github/CODE_OF_CONDUCT.md

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+# Contributor Covenant Code of Conduct
+
+## Our Pledge
+
+We as members, contributors, and leaders pledge to make participation in our
+community a harassment-free experience for everyone, regardless of age, body
+size, visible or invisible disability, ethnicity, sex characteristics, gender
+identity and expression, level of experience, education, socio-economic status,
+nationality, personal appearance, race, religion, or sexual identity
+and orientation.
+
+We pledge to act and interact in ways that contribute to an open, welcoming,
+diverse, inclusive, and healthy community.
+
+## Our Standards
+
+Examples of behavior that contributes to a positive environment for our
+community include:
+
+* Demonstrating empathy and kindness toward other people
+* Being respectful of differing opinions, viewpoints, and experiences
+* Giving and gracefully accepting constructive feedback
+* Accepting responsibility and apologizing to those affected by our mistakes,
+  and learning from the experience
+* Focusing on what is best not just for us as individuals, but for the
+  overall community
+
+Examples of unacceptable behavior include:
+
+* The use of sexualized language or imagery, and sexual attention or
+  advances of any kind
+* Trolling, insulting or derogatory comments, and personal or political attacks
+* Public or private harassment
+* Publishing others' private information, such as a physical or email
+  address, without their explicit permission
+* Other conduct which could reasonably be considered inappropriate in a
+  professional setting
+
+## Enforcement Responsibilities
+
+Community leaders are responsible for clarifying and enforcing our standards of
+acceptable behavior and will take appropriate and fair corrective action in
+response to any behavior that they deem inappropriate, threatening, offensive,
+or harmful.
+
+Community leaders have the right and responsibility to remove, edit, or reject
+comments, commits, code, wiki edits, issues, and other contributions that are
+not aligned to this Code of Conduct, and will communicate reasons for moderation
+decisions when appropriate.
+
+## Scope
+
+This Code of Conduct applies within all community spaces, and also applies when
+an individual is officially representing the community in public spaces.
+Examples of representing our community include using an official e-mail address,
+posting via an official social media account, or acting as an appointed
+representative at an online or offline event.
+
+## Enforcement
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be
+reported to the community leaders responsible for enforcement at
+paula.ruiz.rodriguez@csic.es.
+All complaints will be reviewed and investigated promptly and fairly.
+
+All community leaders are obligated to respect the privacy and security of the
+reporter of any incident.
+
+## Enforcement Guidelines
+
+Community leaders will follow these Community Impact Guidelines in determining
+the consequences for any action they deem in violation of this Code of Conduct:
+
+### 1. Correction
+
+**Community Impact**: Use of inappropriate language or other behavior deemed
+unprofessional or unwelcome in the community.
+
+**Consequence**: A private, written warning from community leaders, providing
+clarity around the nature of the violation and an explanation of why the
+behavior was inappropriate. A public apology may be requested.
+
+### 2. Warning
+
+**Community Impact**: A violation through a single incident or series
+of actions.
+
+**Consequence**: A warning with consequences for continued behavior. No
+interaction with the people involved, including unsolicited interaction with
+those enforcing the Code of Conduct, for a specified period of time. This
+includes avoiding interactions in community spaces as well as external channels
+like social media. Violating these terms may lead to a temporary or
+permanent ban.
+
+### 3. Temporary Ban
+
+**Community Impact**: A serious violation of community standards, including
+sustained inappropriate behavior.
+
+**Consequence**: A temporary ban from any sort of interaction or public
+communication with the community for a specified period of time. No public or
+private interaction with the people involved, including unsolicited interaction
+with those enforcing the Code of Conduct, is allowed during this period.
+Violating these terms may lead to a permanent ban.
+
+### 4. Permanent Ban
+
+**Community Impact**: Demonstrating a pattern of violation of community
+standards, including sustained inappropriate behavior,  harassment of an
+individual, or aggression toward or disparagement of classes of individuals.
+
+**Consequence**: A permanent ban from any sort of public interaction within
+the community.
+
+## Attribution
+
+This Code of Conduct is adapted from the [Contributor Covenant][homepage],
+version 2.0, available at
+https://www.contributor-covenant.org/version/2/0/code_of_conduct.html.
+
+Community Impact Guidelines were inspired by [Mozilla's code of conduct
+enforcement ladder](https://github.com/mozilla/diversity).
+
+[homepage]: https://www.contributor-covenant.org
+
+For answers to common questions about this code of conduct, see the FAQ at
+https://www.contributor-covenant.org/faq. Translations are available at
+https://www.contributor-covenant.org/translations.

.github/DISCUSSION_TEMPLATE/marker-proposals.yml

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+labels:
+  - marker-proposal
+body:
+  - type: markdown
+    attributes:
+      value: |
+        ## 🧬 Marker panel proposal
+
+        Propose diagnostic variants for inclusion in pathotypr.
+
+        The authoritative rules are in the
+        [marker format reference](https://pathogenomics-lab.github.io/pathotypr/marker_format/).
+        The essentials: tab-separated, `position`, `REF`, `ALT`, then **one lineage
+        level per column** root to leaf, then optionally an **empty separator
+        column** followed by `gene` and `mutation`. Positions are 1-based on the
+        single-record reference you name below.
+
+        > **Scope.** Community proposals are currently accepted for the
+        > *Mycobacterium tuberculosis* complex only: *M. tuberculosis*, *M. bovis*,
+        > *M. caprae*, *M. africanum*, *M. microti*, *M. pinnipedii*, *M. orygis*,
+        > and related species.
+
+        When you post, a bot parses the TSV preview and comments with what it
+        found. Editing the discussion runs it again.
+
+  - type: dropdown
+    id: organism
+    attributes:
+      label: MTBC species or subspecies
+      description: Which member or members do these markers target?
+      options:
+        - M. tuberculosis (sensu stricto)
+        - M. bovis
+        - M. caprae
+        - M. africanum
+        - M. microti
+        - M. pinnipedii
+        - M. orygis
+        - Dassie bacillus
+        - Chimpanzee bacillus
+        - M. mungi
+        - Multiple, or the whole MTBC
+    validations:
+      required: true
+
+  - type: dropdown
+    id: panel_kind
+    attributes:
+      label: What do these markers define?
+      options:
+        - Phylogenetic lineage
+        - Drug resistance
+        - Both
+        - Something else, described below
+    validations:
+      required: true
+
+  - type: input
+    id: reference
+    attributes:
+      label: Reference genome
+      description: |
+        The exact sequence the positions were called against. This must be a
+        single-record FASTA when the panel is used. A panel read against a
+        different assembly produces confident, wrong calls with no warning, so
+        please be precise.
+      placeholder: "e.g. GCF_000195955.2 (H37Rv), or the MTB ancestor reference"
+      value: "GCF_000195955.2 (H37Rv)"
+    validations:
+      required: true
+
+  - type: input
+    id: lineages
+    attributes:
+      label: Lineages or phenotypes covered
+      placeholder: "e.g. L1 to L10 and A1 to A4, or L4.1.2, or RIF and INH"
+    validations:
+      required: true
+
+  - type: input
+    id: n_markers
+    attributes:
+      label: Number of markers
+      description: Total rows in the full file, not in the preview below.
+      placeholder: "e.g. 3707"
+    validations:
+      required: true
+
+  - type: textarea
+    id: evidence
+    attributes:
+      label: Evidence
+      description: |
+        Papers, phylogenies, catalogues or other support for these markers.
+        Include DOIs or URLs where possible.
+      placeholder: |
+        - Comas et al. 2010 (doi:10.1038/ng.590)
+        - Validated on 500 RefSeq genomes
+    validations:
+      required: true
+
+  - type: textarea
+    id: tsv_preview
+    attributes:
+      label: Marker TSV preview
+      description: |
+        Paste the first 10 or so rows, tabs intact. The bot validates exactly
+        what you paste here, so paste real rows rather than retyping them.
+
+        The example shows the two shapes: a lineage hierarchy spread across
+        columns, and an annotated row where an **empty column** separates the
+        last lineage level from `gene`.
+      render: text
+      placeholder: |
+        #position	ref	alt	level1	level2	level3
+        615938	A	G	L1
+        1799921	C	G	L2
+        801959	A	G	L2	L2.2
+        2831482	C	T	L2	L2.2	L2.2.1
+        761155	C	T	RIF		rpoB	S450L
+    validations:
+      required: true
+
+  - type: textarea
+    id: full_file
+    attributes:
+      label: Full marker file
+      description: |
+        Drag the complete TSV here, or link a public URL or Zenodo DOI. Proposals
+        cannot be accepted on the preview alone.
+    validations:
+      required: false
+
+  - type: textarea
+    id: validation
+    attributes:
+      label: Validation results
+      description: |
+        If you have run this panel with `pathotypr classify` or `split-fastq`,
+        please share what happened: how many genomes, concordance against what
+        truth set, how many markers were skipped in a `-vv` run, and any edge
+        cases you know of.
+    validations:
+      required: false
+
+  - type: checkboxes
+    id: checklist
+    attributes:
+      label: Checklist
+      options:
+        - label: Tab-separated, UTF-8, with one lineage level per column rather than a semicolon-separated cell.
+          required: true
+        - label: Positions are 1-based on the reference genome named above.
+          required: true
+        - label: Alleles are plain A, C, G and T.
+          required: true
+        - label: I know that indels are accepted by classify and skipped by split-fastq, and my panel is consistent with how I expect it to be used.
+          required: false
+        - label: I have tested these markers on a validation set.
+          required: false
+        - label: I am willing to maintain this marker set.
+          required: false